Science and Inquiry discussion

Another issue that seems to be engaging scientists lately is open publishing? (Is that what it's called?) As I understand it, there is quite a movement advocating for research results to be published on the web where they are freely available to anyone, instead of having to be published in one of the very expensive science journals.

Sounds like a good idea to me, but I'm not a scientist. What are the pros and cons? How do you feel about it?

I can think of two pros and two cons for "open access publishing". The first, and biggest pro: it is much cheaper. Scientists typically pay a hefty amount to get their research published. Then, science libraries at universities and laboratories pay incredible subscription fees for the journals. And this is despite the fact that peer review is provided by scientists for free! Open access publishing reduces the price significantly, often by having a reduced editorial staff, and by publishing online.

The second pro: It is much easier for anybody to get their research published. Which brings me to the first con: it is much easier for anybody to get their research published. The problem is that with open publishing, there is often less editorial and peer review. Now, peer review is not perfect, but it does serve to filter out the non-scientific garbage.

The second con: There are a thousands of con artists out there, actually preying on scientists. They scam scientists by creating an online presence with a journal name that is almost identical to a well-respected journal. This is known as predatory open access publishing. Scientists submit papers to them, and they get published online. But when they don't see their papers published in the expected journals they complain, bewildered.

Overall the benefits will probably outweigh the negatives, but there will be negatives. Some nonsense will be published as scientific fact. However, some controversial information that otherwise would not get a hearing will be validated as new data becomes available.

I'm with David on his points. Even with existing paper journals there have been a number of 'cons' which have made it into print that never should have. I think the open access journals are the way of the future, but we need to make sure they are ethical and focused on true/legitimate science and are above reproach.

Interesting development:

Data blitz is a new hangout (not Hangout On Air), which is hosted by the Science on Google+ Community (http://goo.gl/uhJCN). This monthly hangout will start at 10:00 PM (EDT) on the second Wednesday of each month, and the main goal is to create a platform so researchers can get feedback on their hot off the press research findings and discuss other issues in research, funding, and publishing. There are only two rules. First, to keep things moving, presentations cannot exceed one slide! Second, due to the 10 person limit of hangouts, all individuals who join the hangout will be expected to contribute to the discussion by presenting research or research related issues. RSVP “yes” if you want an invite for the next Science on Google+ Data Blitz.,

Open Access publishing has a lot of pros IMO that people have mentioned, and the cons just aren't that negative to me. Yes, crap will get published, but plenty of that already gets published in peer-reviewed journals. Better to have as much information published as possible, and let time sort out who is correct.

There was a article/blog piece I read yesterday about how everyone is focused on Science and Nature and thus causing a logjam of non-publishing. I think open source can expand the opportunities and address some of the issues but they must somehow maintain legitimate peer review and proper standards. Maybe there need to be some watchdog/oversight group (or maybe there is one already?)

http://www.theguardian.com/commentisf...


There was also this I ran across: http://www.economist.com/news/science...

Time is a natural form of peer review in that if others cannot replicate your work, it is soon forgotten. What else is needed?

The problem is those who would abuse the system. And the harm it could cause in a number of ways.

What kind of abuse are you worried about?

In 2013, Dr. John Holdren, the director of The White House Office of Science and Technology Policy (OSTP), issued a science policy memorandum (http://www.whitehouse.gov/sites/defau...) requiring free public access to the published journal articles of scientific and medical researchers in the United States who received funding from agencies that receive over $1M from taxpaying citizens. This mandate was written in response to an initial online petition on the very same We the People website, called “Require free access over the Internet to scientific journal articles arising from taxpayer-funded research” (https://petitions.whitehouse.gov/peti...).

The petition requests changes that would improve the ability of scientists to verify results published in academic journals. Right now, this is a very large problem. Studies published in top journals, like Nature, Science, as well as the Annals of Applied Statistics, have pointed out serious errors in a number of published papers that have presented, false, misleading, or simply non-reproducible claims. With an estimated spending of $1.5 trillion USD spent globally on research and development, irreproducible results become a serious problem (http://www.scilogs.com/scientific_and...). When those researchers are funded using U. S. taxpayer dollars, it is important that their results are presented fully, in such a way as to meet the scientific “gold standard” of reproducibility. Despite the good efforts of peer reviewers used by journal publishers, journals must issue retractions when articles fail to meet this standard. An article in The Economist pointed out serious flaws in today’s non-reproducible science journal articles and the role that virtual laboratory notebooks could play in monitoring experimental studies:

"Some government funding agencies, including America’s National Institutes of Health, which dish out $30 billion on research each year, are working out how best to encourage replication … Ideally, research protocols should be registered in advance and monitored in virtual notebooks … A rule of thumb among biotechnology venture-capitalists is that half of published research cannot be replicated. Even that may be optimistic. Last year researchers at one biotech firm, Amgen, found they could reproduce just six of 53 “landmark” studies in cancer research. Earlier, a group at Bayer, a drug company, managed to repeat just a quarter of 67 similarly important papers. A leading computer scientist frets that three-quarters of papers in his subfield are bunk. In 2000-10 roughly 80,000 patients took part in clinical trials based on research that was later retracted because of mistakes or improprieties" (http://www.economist.com/news/leaders...).

One major cause of this problem is that when journal articles are published and patents are reviewed, the scientists’ laboratory notebooks are rarely consulted. It is usually only in cases where a litigant challenges a patent that laboratory notebooks have historically held sway. However, the fact that the companies have held the notebooks in their possession, rather than the USPTO, might introduce the possibility for tampering with the evidence should notebooks be required during litigation. It seems to me a much better idea that a neutral third party, the USPTO, would hold a digital copy of these notebooks when a patent is filed in case the need would arise to consult them to prove reproducibility or validate a patent’s claims.

The USPTO already maintains a historical database of full-text US patents to fulfill its Constitutional duties to "promote the progress of science and the useful arts by securing for limited times to inventors the exclusive right to their respective discoveries… Under this system of protection, American industry has flourished. New products have been invented, new uses for old ones discovered, and employment opportunities created for millions of Americans. The strength and vitality of the U.S. economy depends directly on effective mechanisms that protect new ideas and investments in innovation and creativity. The continued demand for patents and trademarks underscores the ingenuity of American inventors and entrepreneurs. The USPTO is at the cutting edge of the nation's technological progress and achievement” (http://www.uspto.gov/about/index.jsp).

Of course, there is a need to protect the intellectual property rights of patent holders for the duration of the patent. Nevertheless, should the product or process described in a patent come under official scrutiny, notebooks should be on hand for official review. Just as articles and data covered in the 2013 OSTP memorandum, the production of research notebooks were also funded by taxes of the American people. These notebooks should, after the life of the patent (usually 17 to 20 years), also become open and freely accessible as part of the public domain and be sustained as part of a U. S. scientific and medical heritage preservation effort. There are a few exceptions wherein material should be restricted—such as national security or technology export limitations— but these materials could instead be transferred at the end of the life of the patent to the National Archives and Records Administration (NARA), where similar documents are housed and accessed through FOIA requests.

How could such a digital notebooks repository database be funded? A financially sustainable project could be achieved through a small filing fee for submitted notebooks, like other fees that fully finance USPTO’s operations (http://www.uspto.gov/web/offices/ac/q...). Unlike other federal agencies, it is a "100%-user fee funded agency" (http://www.ipo.org/index.php/advocacy...), operating without additional taxpayer costs.

We the People allows anyone to create and sign petitions asking the Obama Administration to take action on a range of issues. If a petition gets enough support, the Obama Administration will issue an official response.

Help ensure good science and medicine by signing the petition: http://wh.gov/l5gv0.

Thanks again Shannon. Will take a look at this one.

My colleagues in pharma say only 10% of the top tier journal articles can be reproduced, the rest cannot. And while there will always be mistakes in science, much of this seems to be caused by poor scientific technique.