Tag: open access

Rated my first paper in PLoS One

ResearchBlogging.org

Well, PLoS One has announced its rating system is open. See Chris Surridge’s Blog for more detail here. This is basically the first good system for trying out ratings for scientific publications in much the way it is done at YouTube and other Web 2.0 type systems.

I personally am not sure if I think PLoS One is the perfect system for scientific publishing. But we desperately need to try out new systems and as an Open Access Web 2.0 scientific publishing system, the concept is worth trying. So – I decided to try it.

I rated my first paper. I picked a paper by Xiang Xia Min and Donal Hickey on DNA barcoding. Why did I pick this paper. Well a few reasons. First, when I searched PLoS One for “metagenomics” and “metagenomic” it was one of the papers that came up. As soon as I saw the Barcoding title line I knew I had to look at this paper. Why? Well a few years ago, I posted a “dissent” on Faculty of 1000 about a paper on Barcoding. I stand by my dissent in that article. Basically I said that Barcoding sounded a heck of a lot like what Pace and others have been doing with rRNA surveying of uncultured microbes for a long long time. And it seems to me that the barcoding researchers are rediscovering some of the same findings and challenges that Pace and others found. Of course, not all can see my Faculty of 1000 review. Why? Well it is not Open Access. Bummer. Especially since the response by Hebert was unconvincing too … he basically said that rRNA was not used to delineate species. Apparently he had never heard of phylotypes or any of the extensive work using rRNA to do EXACTLY what they are suggesting mitochondrial genes could be used for in plants and animals.

Anyway – enough about Faculty of 1000. In the new paper, the authors discuss some aspects of barcoding and in particular they address whether one gene can represent all the genes in a mitochondrial genome. Basically, they say yes. But that is beside the point here. You want to know more. Read there paper here. And my comment here. That is yet another benefit of Open Access.

I call on everyone out there to find a paper in which you are interested and rate it and comment on it at PLoS One.

Min, X., & Hickey, D. (2007). DNA Barcodes Provide a Quick Preview of Mitochondrial Genome Composition PLoS ONE, 2 (3) DOI: 10.1371/journal.pone.0000325

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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.

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Support Open Access – write your Congressional Reps

To all supporters of Open Access publications. Please consider writing / faxing your Congressional Reps as there is a lobbying effort going on by supporters of closed access. For more information see the Alliance for Taxpayer Access site.

The most important to write to are the members of the House Appropriations Committee

Nita M. Lowey (NY)
District: http://www.nationalatlas.gov/printable/images/pdf/congdist/NY18_109.pdf
Phone: (202) 225-6506

Rosa L. DeLauro (CT)
District: http://www.house.gov/delauro/our_community.html
Phone: 202-225-3661

Jesse L. Jackson, Jr. (IL)
District: http://www.house.gov/jackson/District.shtml
Phone: (202) 225-0773

Patrick J. Kennedy (RI)
District: http://nationalatlas.gov/printable/congress.html#ri
Phone: (202) 225-4911

Lucille Roybal-Allard (CA)
District: http://www.house.gov/roybal-allard/district.shtml
Phone: (202) 225-1766

Barbara Lee (CA)
District: http://lee.house.gov/index.cfm?SectionID=7&ParentID=0&SectionTypeID=2&SectionTree=7
Phone: (202) 225-2661

Tom Udall (NM)
District: http://tomudall.house.gov/display2.cfm?id=5266&type=KidsZone
Phone: 202-225-6190

Michael Honda (CA)
District: http://nationalatlas.gov/printable/images/preview/congdist/CA15_109.gif
Phone: (202) 225-2631

Betty McCollum (MN)
District: http://mccollum.house.gov/index.asp?Type=B_BASIC&SEC={7744FE23-1C14-4D6C-8864-2271EF5A7DBD}
Phone: (202) 225-6631

Tim Ryan (OH)
District: http://timryan.house.gov/index.php?option=com_content&task=view&id=122&Itemid=11
Phone: 202-225-5261

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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.

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Looming Open Access

People out there who know me know I like to talk. A blog is a perfect outlet for someone who has opinions about just about everything. But my favorite thing about blogging these days is finding other blogs out there that say what I might have wanted to say in a much better and more elegant manner. And this is the case today for Carl Zimmer’s blog on “An Open Mouse.“

Zimmer, for those who are not familiar, is a science writer who also now has a good blog (called The Loom) but is probably best known for his articles in the New York Times and his books. (I have not read all of his books, but his Evolution book is quite good and I have Parasite Rex but alas have not read it yet).

Anyway, Zimmer in his new blog writes about how Open Access science makes his blog easy because he can use a figure from a PLoS paper (on mouse genetic interactions) and rather than sue him, PLoS simply encourages him. I could blather on and on about this (and in fact have – see here for example). But better to just read his words:

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it. In fact, I just did.

I certainly appreciate the importance of copyrights (as the owner of many for my articles and books), but in these situations, keeping information behind a thick wall starts to seem a bit crazy, like the loss of precious bodily fluids. Far from committing some sort of violation to the PLOS paper, I have actually just spread the word about it. A few readers may even go back to read the original. And it was so easy and straightforward for me to do so that I will be very reluctant to bother with anything else.

You go Carl. Welcome to the wonderful world of OA.

——–
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.

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Another way to support open access – call in to radio shows

So – I was driving today from Davis to Walnut Creek to attend the Joint Genome Institutes Scientific Advisory Council meeting (more on this hopefully later as I got lots of good advice from the SAC group which includes George Weinstock, Bruce Birren, Joe Ecker, Mark Adams, and Eric Mathur (who is perhaps the most energetic person I ever met)).

Anyway – on the drive over, I was listening to KQED’s Forum Show and they were doing a story on Avandia, the type II diabetes drug. A recent report on this drug indicates that taking it leads to a significant increase in very negative “side effects” like death. Most interesting and upsetting to me, the lead author of the new study said something to the effect of “our new study was limited significantly because we could not get access to the full results of the clinical trials on Avandia.” This is really stunning. Here is a drug making GSK billions of dollars and yet the clinical trial data that underlies the approval of this drug is not readily available for other people to look at. What is wrong with this picture? I though science was about building on prior results. If you can’t get the data, how exactly do you confirm what someone else did and how do you build on their results? Apparently, medicine does not follow the same procedures.

So I seethed while in the car. And then, I got stuck in a traffic jam (normally I take the train, but was unable to today). And at the same time, they announced the call in number. So I called — the first time I have ever even tried to call one of these shows. And on the second try it rang. And a man answered and asked for my first name and my question/comment. And then, I was on the air … asking about whether there were any attempts to make clinical trial data more readily available (OK, I knew there were attempts, but I was not sure of the details and they needed to be asked on the air anyway).

And if you want to know what I said, and what they said, well listen to the show (I am on at minute ~ 34).

Wed, May 23, 2007 — 9:00 AM
Avandia and Diabetes

Listen Listen (RealMedia stream)
Listen Download (MP3)
(Windows: right-click and choose “Save Target As.” Mac: hold Ctrl, click link, and choose “Save As.”)

And to add to the bonus of being on the air, Jim Bristow, Deputy Director of JGI, was, like me, a bit late to the SAC meeting at JGI. And he came up to me and asked if that was indeed me on the air while I was supposed to be at the meeting. To learn more about clinical trial access, see PLoS Clinical Trials.

——–
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.

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Is Nature going Open Access?

Nature and EMBO are together publishing “Molecular Systems Biology” and all basic research in this journal is Open Access. I am wondering why this has not gotten more press as it seems Nature is experimetning with OA models here. Nature has done some experimentation previously by making certian types of papers available freely (e.g., many genomics papers). But this is definitely one step beyond and they deserve massive kudos for it.

So if you are looking for a new OA journal to submit some systems biology related papers, you should try here. And maybe with a little effort, we can convince Nature it is worth doing for more of their journals.

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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.

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Another education use of Open Access publications

I was reminded of another important use of Open Access publications last week when I gave a talk at Chico State University. Chico St. is one of the California State Universities (I guess it’s formal name is California State University, Chico). The people in the Biology Department there invited me to give a talk (I think this was because of the press coverage of my PLoS Biology paper on the symbionts of the glassy winged sharpshooter – a pest of great concern throughout California since it transmits Pierce’s Disease in grapes).

I had a great visit and a nice drive to and from Chico. I met with lots of faculty doing interesting stuff. And after my talk we went to a local pub with some faculty and students. I had opened up my talk discussing the benefits of Open Access publication and how it was just as important as databases like Genbank (In fact, I think it is a good idea to discuss the importance of OA in scientific presentations in general – spreading the word). And much of our conversation at the pub centered on Open Access.

The most interesting thing I found out was that for one of the journal club/discussion courses that they have there, they only use papers from OA journals like PLoS journals. There were two major reasons for this. (1) As a woefully underfunded university (note – read this Arnold), they do not have funds for their libraries to subscribe to a diversity of journals and (2) using OA publications means they can post all the publications or links to them on a web site for students and do not have to make them closed access / password protected to prevent illicit sharing of non Open publications.

So – another benefit of Open Access publishing. Easing access even o major universities in the US, and making it easier to use research papers as part of course readers and course web sites.

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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.

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open access hits the elections

Well, nice to see OA in the political arena. Obama is asking that the video from the Presidential Debates be released without copyright so that it can be freely blogged, etc.

See the SF-GATE article here.

Obama is quoted as saying

“Rather than restricting the product of those debates, we should instead make sure that our democracy and citizens have the chance to benefit from them in all the ways that technology makes possible.”

I could not agree more. Now if only that were the case for all scientific research.

Thanks to Melinda Simmons for pointing this out

——–
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.

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Nice plea for Open Access in Harvard Crimson

An opinion piece in the Harvard Crimson (student newspaper) by GREGORY N. PRICE and ELIZABETH M. STARK pleas for students to lend more support to the Open Access movement. It is a well thought out piece and worth a look. I particuarly like the proposal for students to make their senior theses available somehow and for students to write letters to Congress supporting OA.

——–
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.

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Jonathan Badger on another reason not to publish in non Open Access journals

Jonathan Badger on his blog has a good little blurb about how he cannot examine a recent piece of research because his institution does not have a subscription to the journal. So the authors lose a reader becuase they published in a non OA journal. Worth a little read for microbiologists since many may not have access to the journal Geology where the paper was published. But the paper was about a fossil that may have been of a fungus.

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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.

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Michael Eisen’s 40th Birthday

Today is the 40th birthday of Michael Eisen, one of the co-founders of PLOS, an ardent supporter of Open Access in science, a top notch evolutionary and molecular biologist, and my brother. Happy Birthday Michael. In his honor, here are some links with information and stories about him:

  • Wikipedia entry
  • East Bay News story about him convincing me to publish in PLOS
  • His lab link
  • A story about his Wired Rave Award
  • A list of those who, like him, have won Presidential Young Career Awards

So if you know him, or even if you don’t wish him happy birthday (here on the blog, or by sending him email. You can get his email address at his lab web page here).

——–
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.

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