Mon 21 Mar 2016 5:08AM

Research publishing in biomedical field moving towards open access

PP Pirate Praveen Public Seen by 249

Research publishing

Taking the online medicine

Old-fashioned ways of reporting new discoveries are holding back medical
research. Some scientists are pushing for change

Mar 19th 2016 | From the print edition

“NEVER tried sharing data like this before,” said the tweet. “Feels like
walking into a country for the first time. Exciting, but don’t know what to

David O’Connor of the University of Wisconsin-Madison was announcing his
decision on February 14th to post online data from his laboratory’s latest
experiment. He and his team had infected macaques with the Zika virus and
were recording the concentrations of virus in the monkeys’ bodily fluids
every day. Researchers know that Zika is transmitted principally by
infected mosquitoes. But if the virus appears in saliva and urine then
these might also be sources of infection.

Dr O’Connor and his colleagues published their results every day to a
publicly accessible website. They hoped this would be useful to others
working on the disease and, ultimately, to health authorities striving to
contain it. They did not expect to garner much attention. But they did.

Within days, researchers from all over the world started contacting them,
making suggestions and asking for samples to conduct work that Dr
O’Connor’s lab was ill-equipped to carry out. He describes the experience
of data-sharing as “universally positive”. But as his tweet suggests, such
openness is far from routine.

Careers in medical research hang on publishing papers in prestigious
journals such as Nature, Science and Cell. Even in emergencies such as the
recent Zika outbreak, or the earlier epidemic of Ebola fever in west
Africa, biologists are reluctant to share data until their work is

Once a paper is submitted to a journal, though, its findings can languish
unseen for months as it goes through a vetting process known as peer
review. Reviewers can ask for substantial changes, further experiments and
also suggest the journal reject the paper outright. If several journals
turn down a paper before it is published, it may be years before the
results become public.

Left in the dark in this way, other practitioners may waste time and money
conducting unnecessary experiments. In cases where the unpublished work
might warn of things like unsafe treatments, the cost of the delay could be
measured in lives. Dr O’Connor’s response is part of a reaction against
this delay.

Peerless publishing

He is not alone. On February 10th, prompted by concerns that vital data on
the Zika epidemic could be held up by journal peer review, scientific
academies, research funders and a number of academic publishers urged
researchers “to make any information available that might have value in
combating the crisis”. The publishers promised that posting a paper online
as a so-called preprint would not disqualify it from publication in a
journal later.

But not all publishers signed up to the agreement, and it raises many
questions. As Stephen Curry of Imperial College London noted in a blog post
for the Guardian, a British daily newspaper, if the approach is valid for
Zika, then why not for other infectious diseases, including malaria or
HIV/AIDS, which kill millions every year?

The problem is not new. But an increase in spending on biomedical research
has led to a surge in scientific publication. The number of research
articles published each year has doubled since 2003 (see chart), with the
biomedical sciences accounting for about 40% of the total.

That has tightened the bottleneck at elite journals, which publish no more
papers than they did 30 years ago and demand that more research be crammed
into each submission. As Ronald Vale of the University of California, San
Francisco, noted last year in Proceedings of the National Academy of
Sciences, an average biology paper in 2014 required two to fourfold more
data than a paper published 30 years earlier. Graduate students at his
institution now take about a year longer, on average, than they did to
publish their first paper.

“The problem is our CV is lagging behind our productivity,” says Jessica
Polka, a postdoctoral researcher at Harvard. To convince people to embrace
preprints, Dr Polka, Dr Vale and other biologists organised ASAPbio, a
meeting held on February 15th-16th in Chevy Chase, Maryland. Their aim is
to get more biomedical researchers to emulate physics, a field in which a
preprint repository has existed since 1991. The arXiv, as this repository
is known, now hosts over a million preprints, a large proportion of which
have been published eventually by physics journals.

Yet, although a poll of nearly 400 scientists attending ASAPbio revealed
90% are dissatisfied with the state of publishing in biology, biomedical
researchers seem reluctant to follow the example of those in the physical
sciences. About 8,000 preprints a month are now uploaded to arXiv. By
contrast, bioRxiv, a similar repository for biology founded in November
2013, holds only around 3,000 in total.

Several things prevent biology and medicine from catching up. First, there
is the fear of disqualification from publication in an elite journal. While
many such journals, including Nature and Science, do allow work to be
published to preprint servers before submission, others do not.Cell, for
example, considers them on a case-by-case basis, asking authors to contact
them before posting online. The Journal of the American Medical
Association, in general, bars such papers from consideration altogether.

A second worry for researchers who post their research online is that they
may be scooped by rivals who could copy their methods and publish the work
in a journal first. This concern could be resolved if funders and
institutions recognised a preprint as the first report of a discovery,
rather than recognising only journal articles. In physics that is already
the case.

Thirdly, there is the danger of non-validated, erroneous findings in a
preprint misleading researchers. However, this has not proved a significant
problem in the physical sciences. Manuscripts submitted to arXiv (and
bioRxiv) are checked to ensure that they are not crank science. And, as
Paul Ginsparg, who founded arXiv, noted in a talk at ASAPbio, researchers
are more careful to check un-peer-reviewed papers before making them
public. Furthermore, journal peer review is not infallible: poor science
routinely slips through the net.

In any case, there is no reason to prevent a preprint from being reviewed
after it is uploaded. One example of this is Discrete Analysis, a
mathematics journal launched on March 1st by Tim Gowers of the University
of Cambridge. This is an “overlay” journal, a sort of stripped-down online
publication which provides links to papers in arXiv and sends submitted
manuscripts out for peer review at no cost to the author (the
administration cost of around $10 per submission is covered by the journal).

Agency of change

Michael Eisen of the University of California, Berkeley, a zealous
proponent of open science, argues that the traditional publication model is
outmoded. Researchers are far more likely to use keyword searches in Google
to find papers relevant to their work than to leaf through printed
journals. Preprints, he says, put researchers back in the driving seat:
“Instead of being told by journals what papers to review, we review papers
useful to us.”

There are signs that researchers might be tiring of the grip that the elite
journals have on the biomedical sciences. Over 12,000 people have so far
signed the San Francisco Declaration on Research Assessment (DORA), which
began in 2012 as a commitment for research to be assessed “on its own
merits rather than on the basis of the journal in which the research is
published”. If the science community takes this notion seriously, more
researchers might be persuaded of the value of publishing preprints
(because journal publications will be less important). A report to the
British government on open access to research, published in February by the
Department for Business, Innovation and Skills, recommends all universities
in the country now sign DORA.

The wide adoption of preprints, however, depends ultimately on paymasters
and interview panels moving away from judging the worth of a scientist by
the number of publications in elite journals that appear on his CV. While
few funding agencies consider preprints to be formally published work, some
have at least made tentative moves towards assessing a scientist’s research
more broadly. Medical research groups in America, Britain and Australia,
for example, have emphasised that scientific work will be judged by its
quality, not by the reputation of the journal it is published in. That will
certainly be more onerous for committees than counting up the “right” sort
of papers. But if more researchers feel comfortable about uploading their
work to preprint servers, it will break the stranglehold of elite journals
on biomedical science and accelerate discovery. That would save millions of
dollars. More importantly, it would save lives.


Pirate Praveen Mon 21 Mar 2016 5:24AM

@soorajkenoth we should try and get universities to sign this lets start from your university. What do you say?