Showing posts with label Peer Review. Show all posts
Showing posts with label Peer Review. Show all posts

Friday, February 23, 2007

Peer Review is changing

Public Library of Science (wikipedia) journal PLoS ONE will use an Editorial Board instead of three luminary boffins (the traditional peer-review model) to Peer Review articles. PLoS ONE is an Open Access Journal - anyone can annotate and discuss articles source: SciAm.

Wired Magazine gave PLOS a rave award in 2004.
PLoS posts new research online, making it available to everyone from high school students to scientists in the developing world. Authors agree to let anyone annotate, excerpt, link, and otherwise add value. And that's not all: Online readers pay nothing so its "open access." Funders of research - usually government agencies - cover the cost of publication up front.

my
highlights / emphasis /
comments

Monday, January 08, 2007

Reforming Scientific and Medical Publishing & Peer Review via the Internet

Reposted from: http://edge.org/q2007/q07_15.html
my highlights in blue

BEATRICE GOLOMB, MD, PhD
Professor of Medicine, University of California, San Diego


Reforming Scientific and Medical Publishing Via the Internet

I am optimistic that the ascendance of open access postings of articles to the internet will transform scientific and medical publishing; and that a number of profound problems—some particular to medical publishing—will be assuaged as a result.

Currently, it can be impossible to gauge the true balance of risks and benefits of medical treatments from a reading of the literature. Frighteningly, this is true too for those doctors who ground their clinical decisions upon a reading of it. I will review some aspects of the problem; and then relay grounds for possible optimism.

First, as is probably true in all fields, bias occurs in favor of existing orthodoxy. This is arguably more troubling in medicine since the orthodoxy is in turn influenced, as has been learned, by the profusion of articles favorable to their products that are ghostwritten by the pharmaceutical industry, or by the for-profit MECCs (Medical Education and Communication Companies) that industry hires for this purpose. These companies in turn pay physicians and pharmacists—including favorably disposed "thought leaders" whom they seek to succor —to be the listed authors, extinguishing any appearance of connection to industry for the favorable views propounded. This provides the appearance that many independent parties are in agreement in their favorable representations of the evidence. Crisply said, advertising is published as though it were science.

These problems are exacerbated by bias arising from direct conflict of interest. Conflict of interest is endemic in medical research; and articles about a class of drug have been shown to be dramatically more likely to be favorable when authored by persons with ties to industry than when authored by persons without such conflicts. Conflicts for authors thus appear to foster submission of industry-favorable articles. Conflicts for reviewers may also foster rejection of industry-unfavorable ones. (As elsewhere, reviewers are drawn from the pool of authors.) Moreover, reviewers are seldom tasked to disclose conflicts, and they remain anonymous, precluding repercussions for biased reviews.

These factors are aggravated, possibly dwarfed, by pharmaceutical company influence on medical publishing—further aligning medical publishing with medical advertising. Medical journals are not the independent arbiters of article quality one might wish. They are businesses and derive their revenue from pharmaceutical company advertising, and from sales to industry of glossy reprints of industry-favorable articles, at inflated prices. For some medical journals, profits reportedly number in the millions, providing high stakes.

At least three former Editors in Chief of major US and British medical journals have penned books decrying the inimical impact of industry influence on medicine. One has to ask why, in medical journals, advertising is accepted (just because it is available for the taking); and whether the journal's bottom line is a proper consideration in dictating what is published, in settings where lives are on the line.

So, whence the optimism? One means to propel optimism is to suggest a tactic that might enable its fruition. Briefly, I suggest that papers be published on the Internet, reviews be submitted by named reviewers; and that others rate (and review) the reviews. Both papers and reviewers receive ratings that are updated on an ongoing basis. While this won't protect against biased submissions, it will protect against biased rejections—and at least enable a voice for original or contrary perspectives.

Until a new systems is worked out, it is probable that more bad science will be released. However the system provides a means for improving poor quality work; and avoiding having to view what remains substandard.

More importantly, more good science may be published—and perhaps, more great science. As Nobelist Sydney Brenner (who famously authored an article entitled "Moron peer review") has observed, many of his co-Nobelists' prize winning work was initially rejected through the review process.

Transformative work by its nature may defy conventional wisdom. One might be drawn to wonder: is there other work that would have revolutionized science and merited a Prize, that languishes unpublished? And that does so because authors at some point ceased to persevere in submission efforts after some number of rejections, or finally deemed the effort to publish futile?

Hark back to the many great discoveries of which we have heard that were initially ridiculed: H. pylori as a contributor to ulcers; handwashing as a means to reduce puerperal fever; the sun as the center around which the earth revolves, to name a few. What might this imply for the possibility that major discoveries may be pilloried into nonpublication by peer review? There is no means to estimate the fraction of Nobel-caliber efforts that achieve publication, as the denominator remains unknowable.

Indeed, the benefits of a new, Internet-based approach may be particularly great for the most important work: work that challenges existing orthodoxy; work that defines a new field and fits no existing journal; work that crosses boundaries to other disciplines—with their own often arbitrary conventions and in-groups; or that demands knowledge from two or more disciplines; science that is ahead of its time, that entails many advances at once or that founds new work on an understanding of relevant material that others do not yet have. Or, too, work that runs counter to vested interest groups—particularly but hardly exclusively in the arena of medicine, where the potent impact of industry influence on information has been the subject of increasing alarm—and where disparities between literature and truth may cost patients' lives.

An instance from mathematics supports the premise that current convention, requiring articles to be published in peer-reviewed journal venues, may inhibit promulgation of at least some of the very most important work. The Poincaré conjecture—a holy grail in mathematics—was recently proved by a Russian mathematician who posted his work on the Internet but refused the bother of submitting his work to a journal. Other cases can be adduced favoring the proposition that some among persons capable of propelling major advances—which often entails rejecting conventions in science—are also constitutionally inclined to reject the conventions, petty obstacles and distractions that attend the current model of scientific publishing. And perhaps they do so with justifiable contempt.

Surely many will defend the current system—not least those who fare well within it, and who benefit disproportionately from it. And surely there will be problems to overcome in the new system. Orthodoxy, in-groups, and interest groups will continue to influence the literature. Those who serve these masters will likely submit negative reviews of articles (and of reviewers) who do not toe the respective party lines. But at least now the contrarian positions will achieve release, reviewers can be held accountable for biased reviews, and unacknowledged conflicts can be exposed in instances when others know of them.

In short, I am optimistic that online publishing, with a review-the-reviewer system akin to that proposed here, will provide more voice and venue for science that may now have the highest need—and the lowest prospect—of being aired.

Humanity's Coming Enlightenment

LARRY SANGER
Co-founder, Wikipedia

Humanity's Coming Enlightenment

I am optimistic about humanity's coming enlightenment.

In particular, I am optimistic about humanity's prospects for starting exemplary new collaboratively-developed knowledge resources. When we hit upon the correct models for collaborative knowledge-collection online, there will be a jaw-dropping, unprecedented, paradigm-shifting explosion in the availability of high-quality free knowledge.

Over the last few years I have received an increasing amount of mail from researchers who want to build dynamic, efficient, and enormous new knowledge resources that follow the wiki model. I believe researchers are drawn to the wiki model because they naturally love several ideas suggested by the model: working closely with large numbers of their colleagues spread over the world; updating shared knowledge on the fly and avoiding costly duplication of labor; presenting knowledge systematically and in all its glorious complexity; and providing clear and compelling free access to important knowledge of their fields to a world that, in many cases, desperately needs such access. These features make the wiki model exciting.

Researchers—scholars, scientists, professionals of all sorts, and indeed, all folks who love books—are, as I say, drawn to the wiki model of strong collaboration in growing numbers. It's an accident of history that methods of strong collaboration online began among programmers and then spread into use by a completely egalitarian community, Wikipedia, and its many imitators. The next step in the evolution, which we are now witnessing on many fronts at once, is the adoption of wikis, and similarly dynamic and efficient "Web 2.0" methods of strong collaboration, by knowledge workers, or (as in the case of my new project, the Citizendium) huge open communities that are gently guided by experts.

I think the most fantastic knowledge resources of the near future will not be encyclopedias or textbooks. They will be brand new sorts of resources, never before possible because they require the participation of thousands, or even millions, of users. What—for example—can that quantity of people do with millions of free books at their fingertips?

Assuming as I do that expert-guided but public participatory free knowledge projects are feasible, and that—after becoming convinced of their tremendous value—millions of intellectuals from around the world will begin spending significant amounts of time developing them together, my considered view is that we are approaching a kind of intellectual revolution:

• The time spent in library, reference, and literature research will be shortened by orders of magnitude, as increasingly detailed indexes and various kinds of maps of the literature are made available, as brilliant new search methods become available for the entire contents of enormous libraries, and as literature reviews (and similar resources) at all levels of specialization are constantly updated.

• Indeed, due to these coming sea changes in the way the results of research are accessed, we might well see new and more efficient methods of presenting novel research to the world than the traditional peer-reviewed research paper. (I suggest nothing in particular here, but as a general point it seems not unlikely.)

• In many fields, especially in the humanities and social sciences, what today appears to be "cutting edge" thinking will be placed into an easily-accessible historical context. It will appear as so much scholarship properly does appear: old ideas warmed-over. I think the embarrassing ease of access to historical precursors and related work will lead scholars in these fields to focus on hard study, consolidation, systematization, and maybe even teaching. Actually, I don't think that. That would be too optimistic.

• There will be—as is already becoming the case—a newly global research community that has a presence coextensive with the Internet itself. This, even more than the advent of the Internet itself, has the potential to bring scholars from developing nations around the globe into the world of research as nothing ever has before. A well-educated, well-plugged-in intelligentsia from every uncensored place on the map could have many remarkable effects.

• Perhaps more important than any of the above, the ease with which information is accessed by teachers and students will require a complete and long overdue rethinking of the methods of education. What happens to education in a world in which not only *some questionable* information is available pretty quickly (as is now the case via Google and Wikipedia), but in which the most "officially" reliable information is available practically instantly to everyone? What would teachers do with their students if class were held every day in the middle of the largest library in the world?

Those are my expectations, and to have such expectations is of course to be very optimistic.

I should add that it seems the management of these information resources will have tremendous power, due to the tremendous value of their resources. So I hope that these managing bodies or persons will use their power according to the love of free speech, Western democratic republican principles of governance, and the rule of law.

Friday, January 05, 2007

the madness of Scientific Method

reposted from Edge.org. Chris Street highlights/edits in bold.

PIET HUT

Professor of Astrophysics, Institute for Advanced Study, Princeton

The Real Purity of Pure Science

I grew up reading heroic stories about progress in science, the absolute superiority of the scientific method, the evil of superstition, and other one-dimensional optimistic views.

Almost half a century later, I have a much more nuanced view of progress, method, and ways of looking at the world. What has been presented as the scientific method, at any given time, has been a simplified snapshot of an intrinsically much more opportunistic enterprise. As such, much damage has been done by suggesting that others areas, from social science and economy to politics, should adopt such a simple and always outdated picture.

The strength of science is not at all its currently accepted method. The strength is the fact that scientists allow the method to change.

The way the method changes is the exact same way through which progress is made by applying the method in doing everyday research. Change of method takes place slowly and carefully, through long and detailed peer discussions, and may be almost imperceptible in any given field during the lifetime of a scientist. The scientific method is like spacetime in general relativity: it provides the stage for matter to play, but the play of matter in turn affects the stage.

The real basis for the success of science is its unique combination of progressive and conservative elements. A scientist gets brownie points for crazy new ideas, as long as they are really interesting and stimulating, and also for being extremely conservative in criticizing any and all new ideas, as long as the criticism can be shown to be valid. What is interesting in new ideas and what is valid in criticism thereof is determined solely by peer review, by the collective opinions of the body of living scientists, not by falling back on some kind of fixed notion of a method.

My optimism is that other areas of human activities can learn from science to combine conservative and progressive approaches, taming the usual black-white duality in a collaborative dance of opposites.

Pure science has been held up as a beacon of hope, as a way to allow scientists to pursue their own intuitions, and thus to find totally new solutions to old problems. This is seen in contrast to applied science, where short-term goals do not allow sufficient room for finding really new approaches. Indeed, the irony here is that the best applications of sciences are ultimately based on pure, rather than applied research.

The moral of the story has been to say that long-term research should not focus on goals, but rather it should let the scientific method follow its own course. Purified from goals, the scientific method is held up as the beacon to follow. But I think this story is still misleading. The greatest breakthroughs have come from a doubly pure science, purified from goals and methods alike. In small and large ways, each major breakthrough was exactly a breakthrough because it literally broke the rules, the rules of the scientific method as it had been understood so far. The most spectacular example has been quantum mechanics, which changed dramatically even the notion of experimental verification.

I am optimistic that all areas of human activities can be inspired by the example of science, which has continued to thrive for more than four centuries, without relying on goals, and without even relying on methods. The key ingredients are hyper-critical but non-dogmatic conservatism, combined with wildly unconventional but well-motivated progressiveness. Insofar as there is any meta-method, it is to allow those ingredients to be played off against each other in the enactments of scientific controversies, until consensus is reached.

Thursday, January 04, 2007

Peer Reviewed Journals - listed at EurekAlert!

What do all of these publishers have in common?

  • ACS Publications
  • AHA Scientific Publishing
  • AMA Publications
  • Cold Spring Harbor Laboratory Press
They all publish Peer Reviewed Journals. Here is a list of over 100 such Journals.

Examples of Peer Reviewed Journals

About EurekAlert!

EurekAlert! is an online, global news service operated by AAAS, the science society. EurekAlert! provides a central place through which universities, medical centers, journals, government agencies, corporations and other organizations engaged in research can bring their news to the media. EurekAlert! also offers its news and resources to the public. EurekAlert! features news and resources focused on all areas of science, medicine and technology.

News by Subject at EurekAlert here.


Wednesday, January 03, 2007

Sense about Science - What is Peer Review?

Chris Street edits in bold (partly) reposted from: Sense about Science - download pdf
"I don't know what to believe" - an article on Peer Review

SUMMARY
•Science has a system for assessing the quality of research before
it is published. This system is called peer review.
•Peer review means that other scientific experts in the field
check research papers for validity, significance and originality –
and for clarity.
•Editors of scientific journals draw on a large pool of suitable
experts to scrutinise papers before deciding whether to publish
them.
•Many of the research claims you read in newspapers and
magazines, find on the internet, or hear on television and the
radio are not published in a peer-reviewed journal.
•Some of this research may turn out to be good but much of it is
flawed or incomplete. Many reported findings, such as claims
about “wonder cures” and “new dangers”, never come to anything.
•Unpublished research is no help to anyone. Scientists can’t repeat
or use it and as a society we can’t base decisions about our public
safety – or our family’s health for example – on work that has a
high chance of being flawed.
•So, no matter how exciting or compelling new scientific or medical
research is, you must always ask…
Is it peer reviewed? If not, why not?
If it is peer reviewed, you can look for more information on what
other scientists say about it, the size and approach of the study and
whether it is part of a body of evidence pointing towards the same
conclusions.

HOW SHOULD YOU MAKE SENSE OF SCIENCE STORIES?
Peer review can help you make sense of science stories as it tells you that the
research has passed the scrutiny of other scientists and is considered valid,
significant and original.
Peer review means that statements made by scientists in scientific journals are
critically different from other kinds of statements or claims, such as those made by
politicians, newspaper columnists or campaign groups. Science is therefore more than
just another opinion.

A SHORT EXPLANATION OF PEER REVIEW
When a researcher, or team of researchers, finishes a stage of work, they usually write
a paper presenting their methods, findings and conclusions. They then send the paper
to a scientific journal to be considered for publication.
If the journal’s editor thinks it is suitable for their journal they send the paper
to other scientists who research and publish in the same field asking them to:
• Comment on its validity – are the research results credible;
are the design and methodology appropriate?
• Judge the significance - is it an important finding?
• Determine its originality - are the results new?
Does the paper refer properly to work done by others?
• Give an opinion as to whether the paper should be published,
improved or rejected (usually to be submitted elsewhere).
This process is called peer review. The scientists (peers)
assessing the papers are called referees or reviewers.

Scientists never draw firm conclusions from just one paper or set of results.
They consider the contribution it makes in the context of other work and their
own experience. It usually takes more than one research paper for results to be
seen as good evidence or accepted as a public truth.

THE SCIENCE PUBLISHING SCENE
For scientific knowledge to progress scientists need to share their research findings
with other scientists. The main way they do this is by publishing their research in
scientific journals – periodical publications intended to further the development of
science by reporting new research.
Journal editors receive many more papers than they can publish, so they use a twostep
selection process. First, they consider whether the paper is a ‘fit’ for their
journals. For example, some journals only publish research papers that are
groundbreaking; others only publish research in a specific area, such as microbiology.
If a journal editor decides that a paper is right for their journal, they send it for peer
review to check whether the research findings are valid, significant and original.

Did you know? There are around 21,000 scholarly and scientific journals that use the peer-review system. A high proportion of these are scientific, technical or medical journals, publishing over 1 million research papers each year.

You are most likely to hear about
new research from the daily news
media, where there is not space or
interest in full references. Good
journalists usually indicate whether
research has been published and
mention the name of the journal.

The more we ask, ‘is it peer
reviewed?’ the more obliged
reporters will be to include this
information.

There is no definitive list of peer reviewed
journals but you can look
up the names of selected peer reviewed
journals online at the
science news service EurekAlert!

SO SCIENTISTS USE PEER
REVIEW, SO WHAT?
When research findings have been peer
reviewed and published in a scientific
journal, this indicates that they are
sufficiently valid, significant and original
to merit the attention of other scientists.
Peer review is an essential dividing line
for judging what is scientific and what is
speculation and opinion. Most scientists
make a careful distinction between their
peer-reviewed findings and their more
general opinions.

Sounds good, but what happens
next?
Publication of a peer-reviewed paper is
just the first step: findings, and theories
about them, must go on to be re-tested
and judged against other work in the
same area. Some papers’ conclusions will
be disputed or further research will show
that they need to be revised as more data
are gathered.

SOURCES FOR FURTHER INFORMATION
Sense About Science: To find out more about peer review you can visit the Sense About Science website where there is a section dedicated to it.

Association of Medical Research Charities: The AMRC has a page, for medical research charities, on the peer review of research grant applications:

Committee on Publication Ethics: COPE provides a sounding board for journal editors struggling with how to deal with breaches in research and publication ethics:

The National Electronic Library for Health: The NELH has a ‘Hitting the Headlines’ archive,
which looks at medical news stories and provides the research evidence on which they are
based

The Science Media Centre: The SMC has published a leaflet, Peer Review in a Nutshell, a guide for scientists preparing for a news interview.

Making Sense of Science Stories - “I don’t know what to believe…”

reposted from Sense in Science

“Is it peer reviewed?” is what Sense About Science is encouraging everyone to ask about science stories. Our short guide, written with input from patients, pharmacists and medical practitioners, among others, lets the public in on the arbiter of scientific quality: the peer review process.

Download the guide (pdf)
Order a copy

During the development of the guide we held workshops for people on the front line of dealing with public concerns, such as doctors and patient groups, and found that they are frustrated by the damage and public anxiety that result from the promotion of poor or unpublished science. Time is increasingly spent trying correct misleading claims found by members of the public on the Internet and elsewhere.

“I don’t know what to believe...” aims to change this by making more sectors of society familiar with what they should ask about research that worries or interests them. It equips people to inquire whether research has passed the scrutiny of other scientists and is considered valid, significant and original.

The guide is being distributed through a campaign involving healthcare providers, Internet sites, helplines and local bodies, based on the ways that people pursue their concerns and interest in particular scientific developments.

Comments on the guide

A guide to help patients

“Rarely a week passes without a ‘miracle heart drug’ or ‘heart scare’ headline appearing in the national media. This can sometimes offer false hope or be very frightening for vulnerable heart patients. We welcome resources like this leaflet, which can help people to read between the lines of newspaper print.”
Jane Shepley, British Heart Foundation

“Whenever there is a story about Alzheimer’s disease in the news the Alzheimer’s Society’s helpline receives calls from people concerned about what they have read. We support anything that helps the general public to understand the health messages they see everyday and encourages people to question the headlines that they read in the popular press. As there is currently no cure for dementia it is disconcerting and disturbing for people with dementia and their families when the results of research are overplayed in the media.”
Joe Crosbie, Alzheimer’s Society

“We encourage initiatives that help the public reach informed judgements about the medical research stories they see and hear in the media. People suffering disease and disability want hope, but not false hope. Action Medical Research aims to have all its work peer reviewed, as a means of ensuring the findings are reported as fully and accurately as possible.”
Andrew Proctor, Action Medical Research

A valuable aid for pharmacists

“Pharmacists are often consulted for their knowledge about medicines and diseases. In their daily work, they often have concerned people asking them about health issues and the latest “miracle cures” featured in the media. This leaflet is a really valuable tool to help pharmacists set these claims into context and explain the role of sound science in making advances in health care.”
John Clements, Royal Pharmaceutical Society

Scientists should be more open about peer review

“Peer review is fundamental to scientific and scholarly communication. But it is also its best-kept secret: outside the scientific community, very few people know what it means or how it works. Sense About Science’s initiative is important because, for the first time, it will help the public to understand the unique character of the scientific process, to ask the right questions of scientists and to engage them with confidence.”
Michael Mabe, Elsevier

Peer review can help the public decide which scientific stories to take seriously

“Sense About Science’s leaflet, ‘I don’t know what to believe …’, will go a long way towards helping the public understand how scientific research is evaluated, and the important role peer review plays in this. By increasing awareness of peer review it will help people decide which scientific stories to take seriously and which to view with caution. When confronted with contradictory or far-reaching claims that may impact their own lives, they will know the questions they need to ask to sift out what is fact from what is just opinion or speculation.”
Dr Irene Hames, Managing Editor of The Plant Journal and author of Peer Review and Manuscript Management in Scientific Journals

A helpful guide for communicating about medical research

“The MRC is pleased to support this guide which is an interesting and useful addition to communicating about medical research.”
Elizabeth Mitchell, MRC

Click here for more comments on the guide and about peer review in general.

Download the guide (pdf, 221 kb)
Order a copy

Saturday, December 30, 2006

Peer Review

Peer review (wikipedia) (known as refereeing in some academic fields) is a process of subjecting an author's scholarly work or ideas to the scrutiny of others who are experts in the field. It is used primarily by editors to select and to screen submitted manuscripts, and by funding agencies, to decide the awarding of monies for research.The peer review process is aimed at getting authors to meet the standards of their discipline and of science generally. Publications and awards that have not undergone peer review are likely to be regarded with suspicion by scholars and professionals in many fields. Even refereed journals, however, have been shown to contain error, fraud and other flaws that undermine their formality.