New Ideas for Scientific Publishing Online

Albert Hybl is an Associate Professor of Biophysics at the University of Maryland who believes traditional scientific publications are often controlled by editorial cliques that don't necessarily select the best or most original articles available. He says that Open Source, Internet-based scientific journals are the wave of the future. Jon Katz touched on this subject last month. Today Professor Hybl tells us exactly how "Slashdot-style" scientific e-publishing could gradually replace the old way, even though, he says, "this will put a lot of Journal publishers out of business, and they're going to do a lot of kicking and screaming before they go." Open Source Scientific Publication Just as Gutenberg is credited for creating the movable type printing press, Harold Varmus, director of the National Institutes of Health, may be regarded as the creator of the E-Library.

The printing press provided a means to distribute multiple copies of political pamphlets, advertising posters, legal documents, novels -- and Journals containing scientific discoveries.

Scientific Societies use these Journals to disseminate research findings. The expense of Society membership and the additional fees for subscription to multiple Journals has gone out-of-bounds for both individual investigators and institutional libraries. It is just not feasible to expect a scientist/researcher or a member of the public to be able to subscribe to all of them or even to a few specialized Journals.

PubMed provides a powerful search engine for locating biomedical articles. PubMed searches are superior to browsing the specialty Journals. However, once you have used PubMed to find an article of interest you must then locate a library housing the Journal in which it appears, that has a Xerox machine with which to make copies of the sought-after articles.

Harold Varmus proposes that an open access e-repository be established to maintain permanent on-line and downloadable archives of scientific literature. The most obvious advantage of this to the researcher is immediate access to any published report via a hyperlink from the PubMed database. E-reports can also contain more information than print Journals, including larger data sets in various formats, pictures with greater detail, or even movies. Many of the costs associated with the publication of a Journal are avoided. Cited literature [footnotes] can also be hyperlinks, which simplifies in-depth background analysis for serious researchers.

Harold Varmus's proposal describes two methods for submission of a new report that could operate side-by-side. The first is to use the established editorial boards, and the second would be through a publicly available preprint repository.

European backers of Varmus's Proposal tend to favor the first, "closed" method of submission. Their claim is that by sticking to the traditional method there is less chance that the database would be flooded by poor quality reports. A subliminal reason for their desire to maintain editorial control might be that delayed publication gives the group that reviews the data extra time to analyze and extract ideas for future research before it is made available to the world.

With the second submission method, each submitted report would only need to be given a cursory review to eliminate voodoo science (SPAM for health care scams or unhealthy foods, etc.) before it was placed, unedited and unreviewed, into the preprint repository, where any interested party could read it. Each "preprint" report could be given a version number like most Open Source Software projects use. Perhaps the "development" version could show editorial strike-outs and new text in different colors from the original. The next higher, "stable" version would be the reviewed, edited, author-corrected copy. Still higher versions might contain supplementary information. Even after they are published, the lower versions should be archived and accessible for historical use.

The Harold Varmus Proposal would require an article to obtain two favorable reviews, perhaps from members of established editorial boards, before it was transfered from the preprint repository to the general repository. Varmus also touches on the possibility of more open reviewing "in which critiques of the scientific reports are accessible and signed." (Today, most scientific papers are reviewed anonymously.) I suggest that, in addition to solicited reviews, signed, unsolicited reviews should also be considered.

Summary

The electronic submission, publication, editing, indexing, archiving, retrieval and utilization of scientific reports, abstracts, and data is taking a significant turn, and Varmus's Proposal may help make that a turn for the better.

I, like Varmus, believe that since most scientific research is funded by the public, the public should have free access to it from open E-libraries via the Internet, and that the only person who should be allowed to claim "ownership" of a scholarly article is the person who wrote it.

No Scientific Society or Journal Publisher should be allowed to hold a copyright on scientific knowledge. The researcher is the only one who has the right to claim, "I discovered it and I reported it."

Comments

Journal Publishers

[nstrug]

The scientific journal publication system is ripe for overhaul. I submitted a manuscript to a journal that shall remain nameless in February this year. Four weeks ago they contacted me to say that the Copyright Transfer form (yes, you have to give them your copyright before they consider publishing) had gone missing and could I please send another one; of course the manuscript was still sitting on the editor's desk. Last week I heard that the paper had been sent to a sub-editor who's job it will be to send copies (that I had to make) to reviewers for peer review. Sometime in early 2000 I will probably get reviewer's comments and amendments. I will then resubmit these and here nothing for another six months. If all goes to schedule the paper _may_ be published by late 2000 - two years after I did the original research. And for all this the journal will charge me (or rather NASA and therefore the US taxpayer) an exorbitant sum - $115 per page and $700 for each colour plate - and as my research area is satellite imagery I can't help but use a lot of colour.

A subscription to this journal, I might add, costs several hundred dollars per year and of course it does not pay any of its reviewers (like most academic journals, it is considered an 'honour' to be asked to review a manuscript.)

Someone, somewhere is making a lot of money out of the whole journal scam.

Nick

Open Source / Open Science

[Bruce Perens]

There's an Open Source / Open Science conference happening in October at Brookhaven National Laboratories, Long Island, New York. I'll be speaking. I expect this to be a discussion topic.

Thanks

Bruce

Slashdot style peer review...

[teraflop user]

I agree that peer-review is vital to filter out crackpots and commercial propaganda. But rather than the traditional editorial board approach, why not slashdot style moderation?

Give each reader and each paper a credibitlty score. The credibility of the reader is based on the average credilibity of each paper they have submitted. Each reader can give a credibility score to each paper they read. The score for the paper will be the submitted scores, weighted by the credibility of each reviewer.

Now it is easy to make foulups in a paper the first time round, so an initial submission could be made to an editorial area. People could add comments slashdot style, and the authors could use these to revise the paper for final submission.

When I started reading this, I hated it. But now I love it! If someone launches a journal in my field this way, I'll gladly submit a paper. Of course, there is no real need to have individual journals, if the database can be searched flexibly.

This has been done in Physics ... no panacea

[StupendousMan]

In the various subfields of Physics, this idea
of a public "preprint server" has been implemented
for some time: check out the Los Alamos
Physics Preprint server.

I've been active in research (astronomy) for
the past ten years or so, and I've had many
conversations with other researchers on the
future of scientific publication. Some of the
main points are:

1. Review/moderation is necessary. There are
a _lot_ of people who have crackpot theories
about the universe, and some of them aren't
shy. Without refereeing of some sort,
the number of scientifically worthless --
see definition below -- papers will grow to
the point that they may swamp the worthwhile
papers. At that point, many users will stop
using the archive.

Note on "scientifically worthless": science
is an enterprise which depends on its
workers to adhere to a set of rules, such
as understanding basic physical principles,
checking the existing literature, creating
falsifiable hypotheses, verifying new
results, repeating experiments, etc. Papers
describing ideas which aren't developed
along these rules are, by definition,
scientifically worthless.

2. Scientists depend on their publication
records to land good jobs, and to advance
in those jobs. At the moment, in astronomy,
at least, the existing
electronic archives are NOT viewed as
"real publications". There's a little bit
of a chicken-and-egg problem: until the
electronic archives are taken seriously,
many people won't publish in them
exclusively. But if everyone publishes
elsewhere, why take electronic archives
seriously?

3. Many people, myself included, worry a great
deal about the use of electronic archives
10 or 20 years hence. I have paged through
bound journals dating back more than 100
years, and used them occasionally in my
research. I can interpret the information
easily. But I don't think it will be an
easy matter to keep electronic media up-to-
date over a century. The librarians to whom
I've talked are _very_ worried about this.

Yes, I know that it may not be difficult
in THEORY to copy old materials to new
formats and new media every N years;
but in practice, it's a royal pain. In an
era of shrinking library budgets, it may
become fiscally impossible.

On the other hand, I do very much support the
idea of "Open Source" publications. It will
enable many more scientists to publish their
ideas. In my field, for example, the authors
have to pay the journals about $125 PER PAGE
for the papers they publish. My last paper cost
over $2000, and I had to pay for some of it
myself (since I work at a small university that
doesn't have a lot of money to support research).

The tricky thing will be to find a mechanism
which keeps the good points of the current
scientific journal system, while avoid the
pitfalls (some of which I've mentioned above).