The Journal Times has a new editorial in support of Open Access publishing.
Key phrase:
While open access to information won’t eliminate the development work, by continuing to limit public access to the information for which the public has paid, we risk losing that vital moment of inspiration which leads to something that makes our lives easier, or healthier, or to a whole new industry. It’s not a risk we can afford to keep taking
I could not agree more.
Well, obviously most people will not want to get one of these “Neglected” tropical diseases, but if you do, one would bet you will be surfing the web trinyg to find out more about it.
And alas, most of the research on such diseases is hidden behind journal restrictions. That was, until now.
Check out the PLoS NTDS Web Site to or Bora’s blog to learn more.
Also check out the editorial by Margaret Chan, the Director General of the World Health Organization. She says
The launch of PLoS Neglected Tropical Diseases marks yet another turning point in the long and notorious history of some of humanity’s oldest diseases. ….
The free availability of leading research articles will benefit decision-makers and diseases control managers worldwide. It will also motivate scientists, both in developing and developed countries.
There is also an interesting population genetic study of Leptospira interrogans.
Good to see this journal out there.
I am posting this which I received in an email.
URGENT CALL TO ACTION: Tell your Senator to OPPOSE amendments that strike or change the NIH public access provision in the FY08 Labor/HHS appropriations bill
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The Senate is currently considering the FY08 Labor-HHS Bill, which includes a provision (already approved by the House of Representatives and the full Senate Appropriations Committee), that directs the NIH to change its Public Access Policy so that participation is required (rather than requested) for researchers, and ensures free, timely public access to articles resulting from NIH-funded research. On Friday, Senator Inhofe (R-OK), filed two amendments (#3416 and #3417), which call for the language to either be stricken from the bill, or modified in a way that would gravely limit the policy’s effectiveness.
Amendment #3416 would eliminate the provision altogether. Amendment #3417 is likely to be presented to your Senator as a compromise that “balances” the needs of the public and of publishers. In reality, the current language in the NIH public access provision accomplishes that goal. Passage of either amendment would seriously undermine access to this important public resource, and damage the community’s ability to advance scientific research and discovery.
Please contact your Senators TODAY and urge them to vote “NO” on amendments #3416 and #3417. (Contact must be made before close of business on Monday, October 22). A sample email is provided for your use below. Feel free to personalize it, explaining why public access is important to you and your institution. Contact information and a tool to email your Senator are online at http://www.taxpayeraccess.org/nih/2007senatecalltoaction.html. No time to write? Call the U.S. Capitol switchboard at (202) 224-3121 to be patched through to your Senate office.
If you have written in support before, or when you do so today, please inform the Alliance for Taxpayer Access. Contact Jennifer McLennan through jennifer@arl.org or by fax at (202) 872-0884.
Thanks for your continued efforts to support public access at the National Institutes of Health.
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SAMPLE EMAIL
Dear Senator:
On behalf of [your organization], I strongly urge you to OPPOSE proposed Amendments #3416 and #3417 to the FY 2008 Labor, Health and Human Services and Education Appropriations bill (S.1710). These amendments would seriously impede public access to taxpayer-funded biomedical research, stifling critical advancements in lifesaving research and scientific discovery. The current bill language was carefully crafted to balance the needs of ALL stakeholders, and to ensure that the American public is able to fully realize our collective investment in science.
To ensure public access to medical research findings, language was included in the in the FY 2008 Labor, Health and Human Services, and Education Appropriations Bill directing the NIH to make a much-needed improvement to its Public Access Policy — requiring that NIH-funded researchers deposit their manuscripts in the National Library of Medicine’s online database to be made publicly available within one year of publication in a peer-reviewed journal. This change is supported by NIH Director Elias Zerhouni, and a broad coalition of educational institutions, scientific researchers, healthcare practitioners, publishers, patient groups, libraries, and student groups — representing millions of taxpayers seeking to advance medical research.
Amendment #3416 would eliminate this important provision, leaving only a severely weakened, voluntary NIH policy in place. Under the voluntary policy (in place for more than two years) less than 5% of individual researchers have participated — rendering the policy ineffective. The language in Amendment #3417 would place even further restrictions on the policy, ensuring that taxpayers – including doctors and scientists – are unable to take full advantage of this important public resource.
Supporting the current language in the FY08 LHHS Appropriations Bill is the best way to ensure that taxpayers’ investment in NIH-funded research is used as effectively as possible. Taxpayer-funded NIH research belongs to the American public. They have paid for it, and it is for their benefit.
I urge you to join the millions of scientists, researchers, libraries, universities, and patient and consumer advocacy groups in supporting the current language in the FY08 LHHS Appropriations bill and require NIH grantees to deposit in PubMed Central final peer-reviewed manuscripts no later than 12 months following publication in a peer-reviewed journal. Vote NO on Amendments #3416 and #3417.
While at the GME meeting – I have now been approached by 3 people saying they really liked the discussion I initiated on PLoS One for a paper on metagenomics a few weeks ago. They were not saying they liked my comments but that there was an active discussion about some important topics. I think the function on PLoS One has great potential to engage the broad scientific community in discussions that might have previously been limited to journal clubs. So it is nice to see (1) that people are reading stuff on PLoS One and (2) that they seem to like the commenting function.
U. C. Davis, where I am a faculty, is recruiting nominations and applications for “PROVOST AND EXECUTIVE VICE CHANCELLOR.” So if you are itching for something new out there, and think you have what it takes, consider applying.
Oh, and hopefully, from my point of view, you will be more supportive of Open Access publishing than our interim Provost and Executive Vice Chancellor, Barbara Horwitz (see here and here for more on her position on Open Access).
Let me state first, that I realize that Open Access is not the only important thing in the world and that there are many kinds of OA and furthermore that some people may generally support OA but may be worried about how to get there (e.g., see Timo Hannay’s discussion of some of his concerns about doing full OA here ).
And Dr. Horwitz has done some quite good things in other aspects of her job. But her more recent foray into the OA debate was so icky, so misleading, that I am really hoping she does not become full time provost and furthermore that whomever does has a different take on the whole thing.
What was it that raised my ire? Well, she was directly involved in what could be considered a bit of a test run of the ideas behind PRISM, the much panned “coalition” against open access. I wrote about the PRISM-esque test run by Horwitz and colleagues here. In summary, she and a group of other anti-OA advocates wrote a letter stating their PRISM-esque objections to the OA movement. For example here is one of their PRISM-esque quotes
“The free posting of unedited author manuscripts by government agencies threatens the integrity of the scientific record, potentially undermines the publisher peer review process, and is not a smart use of funds that could be better used for research.”
Ooh you say — a letter — what’s the big deal. Well, the ten people who wrote the letter wrote it as individuals, but then a PRISM-esque anti OA group wrote a press release wherein they referred to the people who wrote the letters as “University Officials” which they were (all were deans, provosts, etc) and how University Officials were against OA. This was clearly done to give the impression that the Universities themselves were against OA, which was not true. And this misleading presentation was clearly done in collaboration with the letter writers. So Horwitz and crowd allowed the fact that they were University officials to be used to mislead people into thinking that their opinions were POSITIONS of the university.
Horwitz is welcome to her opinions and I agree with Timo Hannay that we need a fair and measured debate about OA (although I think he goes overboard in dinging people for being a bit agressive in their blog commentaries about it — this is after all what makes blogs a bit fun). But let’s not abuse our positions of authority and responsibility within the University to mislead about our positions. And just because we have a pleasant debate does not mean I will support an anti OA advocate to help run UC Davis, not that I have much say in the matter.
But given that U. C. Davis is strong and getting stronger in the sciences means that one key aspect of the recruitment of a new Provost and Executive Vice Chancellor should be how they stand on scientific publishing.
I got this by email and figured I would post it here.
Senior Scientific Editor, PLoS Biology – based in San Francisco
The Public Library of Science (PLoS) seeks an experienced editor and manager to lead its flagship life science journal – PLoS Biology – in San Francisco. Since its launch in 2003, PLoS Biology has rapidly become established as both a high impact journal and a leader in the open-access publishing movement. This is a unique opportunity to develop a ground-breaking journal, and to shape a fundamental transition in scientific publishing.
The primary responsibilities of the job will be:
· Oversight of all editorial aspects of the journal, including peer review of research articles and commissioning of additional content. This includes fostering a collaborative decision-making process among in-house editors and the editorial board
· Management of the journal editorial staff
· Working with the PLoS leadership and the journal team to determine journal strategy within the context of our publishing portfolio and open-access goals
· Leading the further development of the journal specifically as we introduce web features that will allow greater user participation
· Attending scientific conferences and outreach to the scientific community, representing PLoS Biology and the broader aims of open access
Required experience and qualities:
· Extensive experience handling peer review of primary research
· Substantial management experience, and excellent communication skills
· Broad knowledge of the biological sciences, with a network of contacts in the scientific community
· Knowledge of and interest in the changing nature of scientific publishing, particularly in an online environment
· Strong commitment to open-access publishing
· Willingness to be flexible to accommodate time differences between our international offices
Application Procedure
PLoS offers competitive salaries, a creative and casual work environment as well as a full range of comprehensive benefits, including medical; dental and vision; life, LTD and STD coverage and a matching 401k program. If interested, please send resume and cover letter to jobs@plos.org and use “Managing Editor, PLoS Biology” as the subject of your email. Informal enquiries may be made by email to the Director of Publishing, Mark Patterson – mpatterson@plos.org. Principals only – email from recruiters will be ignored.
If you have not seen the wonderful news about the latest anti Open Access initiative called PRISM, well you should surf around the blogosphere a bit. PRISM is a group started by the AAP – the Association of American Publishers that – there is no nice way to put this – is a sad stage in the evolution of publishing. Basically, it is a Macarthy-Era ripoff where Open Access is the new evil that communism once was. And everything wrong with the world is in essence blamed on the Open Access movement. For more detail on PRISM, and what is wrong with it, including the pirates use of copyrighted material, see some of these links:
I think academics and the public need to fight back against this attempt to mislead the public about the issues surrounding Open Access publishing. And one way to fight back is to recommend that the members of AAP drop out or request termination of the PRISM effort. So here is a list (see below for the full list) with links of the members of AAP. If you are involved or have connections to any of these groups, consider writing or calling them and suggesting they reconsider involvement in AAP. Look, for example at all the University presses. If they do not back out of PRISM we should consider launching a boycott of AAP members.
Full list of AAP from the AAP web site:
Academic Learning Company, LLC
Aequus Technologies Corporation
Al-Basheer Publications and Translations
American Academy of Pediatrics
American Association of Cancer Research
American Association of Pharmaceutical Scientists
American Foundation for the Blind
American Institute of Aeronautics and Astronautics
American Psychiatric Publishing, Inc.
American Psychological Association
American School of Classical Studies at Athens (The)
American Scientific Publishers
American Society of Clinical Oncology
ASIS International
Association for Computing Machinery (ACM, Inc.)
Association of Research Libraries
Athena Media, Inc.
Barnhardt & Ashe Publishing, Inc.
Cadmus Professional Communications
Capitol Books
Cold Spring Harbor Laboratory Press
Colorado Independent Publishers Association
Cornell Maritime Press
Council on Foreign Relations Press
Council on Library and Information Resources
Cover Publishing Co.
Earthquake Engineering Research Institute
Emida International Publishers
Ernst & Young, LLP
Federation of American Societies for Experimental Biology
Focus Publishing/R. Pullins Company, Inc.
Fulcrum Publishing
Gallaudet University Press
Haiduk Press
Hampton-Brown Company, Inc. (The)
Health Affairs/Project Hope
Hearst Book Group
Hispanex, Inc.
Institute for Electrical and Electronics Engineers, Inc. (IEEE)
Institute for International Economics
Institute for Scientific Information
Institute of Physics Publishing
Instrumentation, Systems, and Automation Society (The)
The Institute, Inc.
J. Paul Getty Trust Publications
James A. Rock & Company Publishers
Key Education Publishing Company LLC
Kirchoff/Wohlberg, Inc.
Library of Congress Publishing Office (The)
Lidenmeyr Book Publishing Papers
Lippincott Williams $ Wilkins Journals
Massachusetts Medical Society/New England Journal of Medicine
Medical Group Management Association
Minnesota Historical Society Press
Modern Language Association of America
Mooring Field Books, Inc.
Morgan & Claypool Publishers
National Computer Systems/Pearson
National Education Standards
National Publishing Co.
National Science Teachers Association (NSTA)
New England Journal of Medicine
Pan American Health Organization
Pennsylvania State University Press (The)
Pillsbury Winthrop Shaw Pittman, LLP
Pub Smarts, LLC
Publisher’s Group Incorporated
Publishing Illuminations
Rainbow Books, Inc.
Ray of Light Publishing Company, Inc.
Recording for the Blind and Dyslexic
Resolve Corporation
Saferock USA, LLC
Scholatic Testing Services, Inc.
Scientific American/St. Martin’s College Publishing Group
Teachers College Press
Tighe Publishing Services, Inc.
Tribune Education
The University of Hawaii Press
University of California Press
University of Illinois Press
Whitston Publishing Company, Inc.
I just came across this web site for something called the “Partnership for Research Integrity in Science and Medicine.” I looked through it an thought – this must be a spoof. A good April 1 joke about the dinosaurs of the publishing industry. The reason it seems like a joke is well, the stuff there is so incredibly inane as to make one laugh. In essence the whole site is an anti Open Access site. They are against Open Access to publications it seems because Open Access does things like
I could go on and on about the silly stuff there … but lets just say that everything on the site seems like a spoof. But alas, it is not. PRISM is for real. It is the last gasp of a dying breed – publishers who refuse to do what is the right thing for science and society. Yes, I understand there are some issues with Open Access that still need to be solved. But this McCarthy like tone of PRISM – basically equating openness with evil and godlessness is ridiculous. I think this is a sad day for the people behind PRISM – the AAP (Association of American Publishers). I am sure they have done some good things over the years. This is certainly not one of them and a good sign that anyone out there with any common sense who might be involved in AAP should get out or fight for change within the institution.
For more on Prism see
Normally I avoid writing about discoveries in non Open Access journals. But I cannot help myself here. On Friday a wickedly cool paper was published in a journal that I will not name here. In this paper they describe a new bacterium: “Candidatus Chloracidobacterium thermophilum.” It is REALLY rare for a new bacteria to be described in a journal like this one. How did they get it in this journal? Well this organism represents the first new photosynthetic lineage of organisms discovered in many many many years. The bacterium is in the phylum Acidobacteria and can carry out aerobic photosynthesis. Prior to this discovery, photosynthesis was only known in five evolutionary lineages – all of them bacteria: Cyanobacteria, Chlorobi, Chloroflexi, Proteobacteria and Firmicutes. Photosynthesis in plants, algae and other eukaryotes all came from symbioses with cyanobacteria to these five groups represented the only “primary” photosynthetic lineages. Thus it is a big deal to find a sixth lineage having photosynthesis.
And – here is the fun part. How did they find this? With the help of metagenomics.
Only five bacterial phyla with members capable of chlorophyll (Chl)–based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)–synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. “Candidatus Chloracidobacterium thermophilum” is a BChl-producing member of the poorly characterized phylum Acidobacteria.
That is, they saw the first hints of this through analysis of metagenomic data which was generated by isolating DNA from a Yellowstone hot spring and sequencing the snot out of it. Anyway – as some might have guessed – my only lament about this paper is that it is in a non Open Access journal (I tried to convince the lead author to submit elsewhere but was not convincing enough I guess). It really is too bad – it would be nice to post some of their figures here for others to look at and it this paper would make a great one to use for educating the public about metagenomics. But alas the public cannot get this from Science for at least 1 year and bloggers and other news sources cannot really run with the story because of the copyright limitations. So – great science and great example of the power of metagenomics but restricted public use.
I know a lot has been written in support of Open Access publishing and Open Science but I must say this paragraph (from MungBeing magazine by Andrew Hessel) is one of my favorites is more over the top than I initially realized,
Garage Biology and Open Source Biology: Twenty five years ago, kids flocked to computers, pushing the limits of what they could do. Similarly, the next generation of genetic engineers won’t need laboratories or even PhD: they’ll have laptops, cheap mail order DNA synthesis, and, thanks to Google and Wikipedia and open journals like PLOS Biology, access to mountains of free biological data. They’ll work in basements, garages, and cafes, and they’ll trade ideas and collaborate on genetic designs the same way open source programmers now write computer code. Keep in mind that it was only 30 years ago that a little company called Apple started out of a California garage.
Thanks to Bill Hooker’s blog response for calming me down a bit about how brilliant this quote is. The main issue I have is that there are risks associated with genome engineering that are different and more substantial than those associated with piecing together computers here and there.
Jonathan Eisen's Lab 