To cite this article : R.E. Dessy, Trends Anal. Chem., 19 (2000) 587(–592)
Chemical E-Preprints: The Ostriches
Posted 12 July 2000
Ray Dessy
Chemistry Dept. 0212
Virginia Tech
Blacksburg, VA 24061
PROLOGUE
This article examines the current and future state of electronic preprints in chemistry. Their time has come — yet some resist, others are ambivalent, and many chemists do not recognize past successes. We'll examine the background and vocabulary of the area, look at the politics involved, revel in what e-preprints may bring, and contrast two cultures under stress and facing inevitable change.
Some 2400 years ago, Aristophanes wrote a series of Greek comedies that exposed the foibles and absurdities of his society. His Early Comedy did not criticize the basic concept of Hellenic culture, but rather focused on illogical, reactionary, conservative or absurd implementations, and the associated personalities. Those plays — The Wasps, Birds, Clouds, Frogs, Knights — won the ear and mind of the society of citizens who were living through dramatic changes in their world. These changes were linked heavily to an inability to resolve internal political differences, coordinate actions, encourage fealty, and use knowledge wisely. In Aristophanes world, it all culminated in the defeat of the Athenian forces at Syracuse, ~415 BC 1, and eventually the transformation of the classic individualistic Hellenic city-states to the Hellenistic period's vibrant nation-states. Only eleven of Aristophanes comedies have been preserved.
These Early Comedies were works of frank, extreme satire, scurrilous and lampooning in nature. But there always was an underlying political/social message that is relevant to this article on e-preprints. Fragments of a 12th comedy by Aristophanes have recently been found behind a photocopier at the Classe Museum near Ravenna. Entitled Ostrich (Strouqoj), the prologue, parabasis, a few lyrics and lines, and the last scene are all that survive. But they help us analyze what is happening in chemical e-preprints in the new millennium.
Today, we society of chemists face a critical period in our technical literature brought on by politics, economics, management styles, and new technology, described as follows by John Perry Barlow:
"Since we don't have a (perfect) solution to what is a profoundly new kind of challenge, and are apparently unable to delay the galloping digitization of everything not obstinately physical, we are sailing into the future on a sinking ship. This vessel, …, was developed to convey forms and methods of expressionentirely different from the vaporous cargo it is now being asked to carry. It is leaking as much from within as without. Efforts to keep the old boat floating are taking three forms: a frenzy of deck chair rearrangement, stern warnings to the passengers that if she goes down, they will face harsh criminal penalties, and serene, glassy-eyed denial." 2
PARABASIS
Nowhere is this problem more frustrating and vexing than in the area of electronic preprints for chemistry. Aristophanes would say that some publishers, some societies, and many scientists, are Ostriches, with their heads buried in the sands of change, and their nether regions exposed to violent bouts of a blustering Mistral.3
The Past: E-preprints are not new. They were one of the original driving forces behind the Internet. High-energy physicists and astronomers wanted ways to exchange data and papers quickly in "hot" areas. Readers unfamiliar with the area can see splendid examples on the WWW.4 Many critics of e-preprints often cite the sociological differences between physics and chemistry. These reactionaries claim that the former are a small, tight-knit group where common target areas, a well developed sense of caveat emptor, and critical damping of errors due to quick detection of faults in thought and deed, result in a self-policing arena. They conclude that e-prints would not work in chemistry.
Such critics of e-preprints in chemistry fail to realize that one of the results of the increasing number of productive chemists is the development of isolated condominium-groups whose members share a very localized interest area. The days of chemists who read JACS from cover-to-cover are gone. Specialized journals, tightly targeted symposia, and global-village clans are common. And modern search engines and database structuring makes it possible to finely select the subset of e-preprints offered to a researcher. For example, a search of the Web of Science (Institute for Scientific Information®) with the Boolean "glucose AND sensor AND in vivo" returns only ~150 papers out of ~11,000,000. To be useful, the successful e-print server will require Boolean key-word, word adjacency/proximity, and tile-bar search strategies5 but, successful e-print servers do not require an intimate clique of compatriots — that is a yearned for myth.6
The Present: In the print world, the number of papers being submitted exceeds the ability of existing media to absorb them. As individual print subscription numbers decrease, and institutional subscriptions drop, the editors and publishers of the classic journals are faced with an increasing number of paper submissions and a slowly increasing or static printed-page count.
Young workers, with little established track record, find it hard to place printed papers in the top tier journals — those with a perceived better "quality" or "Citation Index"® figure of merit. Department Heads and Promotion & Tenure Committees are both guilty of counting papers and multiplying by some "citation index" figure, rather than attempting to read and understand the published work itself. The fledgling author may choose to place the paper in a second tier specialized journal, jeopardizing his career evaluation and perhaps missing some segment of his peer group who do not subscribe or routinely read the publication.
E-preprints could be the equivalent of MP3 for young scientists — quick, inexpensive exposure that can also help spread knowledge.
Print media, constrained by page count and print costs, also eschew some of the brilliant features that the html/xml world can bring to such manuscripts. These multi-media tools add clarity, usefulness, and readability to any scientific manuscript. For a delightful example, visit the Internet Journal of Chemistry.7
Scientists as Critics: Reactionary critics always focus on the importance of the peer review process in maintaining quality in chemical literature. Peer review has never been without its problems. New ideas, or ideas that conflict with the mind-set and set-mind of the reviewer have always faced difficulty. Harold Zeiss, a chemist at Monsanto's Mound Laboratory, many years ago was interested in the colored crystals found at the top of smoke-stacks. His attempts to publish a paper describing a novel bonding system involving cyclopentadiene rings and metal atoms was repeatedly rejected by an ACS journal. A few years later E. O. Fischer's papers were accepted, and the rest is history — Fischer's well-deserved 1973 Nobel Prize, which he shared with Sir Geoffrey Wilkinson. J. Kollonitsch, at Merck, discovered that organocadmium reagents do not react with acid chlorides to produce ketones. His manuscript was rejected by an ACS journal, due to a referee who was in the process of publishing paper ~LXIX in his long-published series based on just this reaction. The chemical solution to the dichotomy — Kollonitsch had shown that the reaction only occurs in the presence of a Lewis Acid catalyst. Since the organocadmiums were usually made from cadmium halides and Grignard reagents, the needed catalyst was always there. The reviewer's ego solution drove the paper to Nature, which at that time was not a high impact chemical publication. It took years for the concept to seep into textbooks.
Many referees also assume the anonymous mantle of a music or art critic; and the goal is to produce a report that expands the apparent erudition of the creator, rather than assisting the author. The society of chemists may overestimate the importance of the filter function proffered by referees.
Imagine what Aristophanes, in his comedy The Ostriches, would do with a current "paper reviewer" who has proposed a non-refundable reviewer's fee, to be shared with the editor and the reviewer. This fee is suggested to be scaled to the impact index of the journal. To quote "The emergence of electronic publishing, changing distribution patterns, and the increasing proliferation of papers and journals clearly define a new economic paradigm in which journals operate. It is high time to recognize that the referees are an essential part of this game (sic) and that their services should be rewarded like those of any other professional."8
"Authors write to know that they are not alone;
Critics write to assure themselves a home." (Ostriches) 9
The Chemical Future: Generational changes, involving the Internet, suggest that no harm, except to incautious authors, would result from e-preprints. Web readers already accept a caveat emptor world. Submission of too many poor papers, or a single badly flawed MS, would quickly degrade reputations. "Publish or perish; but substantiate or suffocate!" The rapid communication pathways available to correspondents today — via e-mail, forums attached to the e-preprint itself that can accept readers observations and criticisms, and the ability to re-post corrected copies — can lead to a refining process that provides the fastest possible route to a useful literature contribution.
The rapidity of the process would permit young, competent workers to start the creation of an external image swiftly. Building such an image via traditional print media is harder today than in the past, and the older community of professionals needs to change its habit patterns to recognize this fact. There are just too many papers, more competition, and less paper space.
With e-preprints, P&T Committees and evaluation panels would have Web access to the open criticism and positive responses of all interested peers, helping them to analyze a candidate. Too often these evaluation groups have relied on a small number of "selected" outside peer reviewers. The capricious nature of these few peer reports has endangered many a career.
OSTRICH EGGS and KANGAROO POUCHES
The prologue of The Ostriches suggests a comedy that focuses on a world of fantasy inhabited by two species of animals, ostriches and kangaroos.10 The ostrich, faced with a changing environment, chooses not to experiment, and continues to practice thrusting its head into the sand or a bush when being overtaken by pursuers, through incapacity to distinguish between seeing and being seen. In some sense this might be seen to reflect an attitude encompassed by a recent quote attributed to Robert Bovenschulte11— "For two years the American Chemical Society's Publications Division has considered setting up (an e-preprint) system. … The ACS editors are concerned about the impact of e-preprints on the society's "prior publication" policy, which prevents journals from accepting work that has been published previously elsewhere."
"All woe to those who first reside upon the Web,
They won't print here, but must find someplace else
instead."12
The kangaroos of Ostrich, faced with change and ecological pressures decide to adapt, experiment, and produce rock wallabies, tree kangaroos, brush and forest kangaroos, wallaroos, and quokkas. This attitude reminds one of Casio who, 20 odd years ago, experimented with ~128 models of electronic keyboards in order to understand where the emerging market might lead. Their initiative helped capture a major market share and changed the sound of music forever. Another example is ChemWeb.com's experimentation with new chemical e-publishing forms, and particularly chemical e-preprints (vide infra). Experimentation is evolution's tool.
"Oh joy to they that share their work upon the Web;
Each thread makes strong the sparkling spider-web."
FOOTPRINTS, NOT IN "PRINT"
For both critics and supporters of e-preprints, the literature is replete with examples from other fields of science that suggest that any associated problems do have solutions, and the approach has many benefits.
Electronic preprints present new challenges for bibliographic control. The pace of scholarship and access has changed irrevocably. Since there are an average of three full-text revisions in pre-publication processes, due to reader commentary and author response, a seamless integration of all e-publishing is required.
Listen to a voice from 1998 — "It is now the time to develop a complementary system of electronic information for the distribution of preprints and technical information, a system that can ultimately be fully integrated with the formal (electronic and print) publication of refereed papers. The electronic journals will not eliminate the need for preprints. In the astronomy community peer review continues to play a key role in the formal publication process, but the preparation of papers for publication, including both quality "typesetting'' and preparation of the electronic presentation format (including the addition of hypertext links, back- and forward-references), is time consuming. Authors desiring truly rapid dissemination of their research still want to issue preprints. But without the indexing facilities that have been provided for paper publications and the electronic journals, many of these e-preprints are difficult to locate. In order to take full advantage of the WWW, we require a truly distributed electronic document index and search facility, a system that is dynamically updated and simple to (use)".13
All e-preprints may change in wholesale ways, not amenable to corrigenda the way published papers are, and one expects them to go through several versions up to the published paper, which then remains fixed. Without a reliable tracking mechanism it can be almost impossible to tell the lineage of an electronic document. The solution — track a preprint through the publication process, so that it can automatically be identified with the published paper using meta-tags and URL pointer/resolvers. The search system returns the URL of the preprint until the paper is published, and the URL of the electronic journal article afterwards. At that point the e-preprint "disappears" since it is almost undiscoverable, and may be dismounted.14 Existing LANL and NCSTRL systems use such meta-data information.4
As an added feature to an e-preprint service, it is simple to provide a basic notification service. This service allows users to register an interest profile with the server. On a regular basis — daily, weekly — the database could be searched for new preprints that match the user's profile, and e-mail messages sent to the user notifying them about the new articles.15
Enriched linking poses interesting possibilities and challenges. Schematics, images, technical data, or raw and analyzed experimental data are all feasible and useful. Such value-added efforts require a web of cooperation between author, server personnel, and users. Mark-up languages need to be defined, controlled, and monitored.
It is essential that the growing ocean of protean information be integrated into traditional models, but the adventure may morph into a new format as scientists learn how to use the medium. The methods of control and fiscal support will soon become important. How does one assure long-term mounting? Will the system eventually involve pay-per-view, or a giant scholarly repository. Will the system lead to Islands of Filtered Information that isolate the reader?16 At the bleeding edge, will traditional publications disappear? Will the operators of the e-preprint server expect to receive first-refusal e-journal rights and copyright? Although the Cuisinart™ potential and the availability of new multi-media make new shapes unsettling for some, there is tremendous potential for evolving new systems to meet new needs. Scientific articles may eventually cease to be linear, but become multi-threaded experiences.17
Change: The previously antagonistic attitude of many publishers to the prior electronic publication of articles has become more liberal over the past few years. Publishers that refuse a priori to publish articles that have been posted on e-print servers appear increasingly isolated — they seem to live in one of Aristophanes' fictional fantastic lands, Cloud Cuckooland (Nephelokokkugia).18
Nature, the Journal of Neuroscience and many other journals have stated that posting on e-print servers does not a priori constitute prior publication, but is rather a legitimate means of communication between researchers.19 The British Medical Journal joined their ranks. In an editorial, Richard Smith, its editor, argues that journals have nothing to fear from e-print servers. "Strong publication is associated with prestige, credibility, reliability, wide availability, news coverage and permanence... [scientists] want to publish both on e-print servers and in peer-reviewed journals. It's not either/or, but both."
Several journals, including the BMJ, have experimented with making manuscripts available on the web before they have been peer reviewed, and then subjecting them to open, online virtual peer review. A pilot test on one article prompted a large response from readers. Tony Delamothe, deputy editor, admits that the opinions expressed were of variable quality, but believes that they nonetheless allowed conclusions to be drawn as to whether the paper should be accepted for publication. 20
There is a strong connectivity between today's emerging e-publishing arena, and the changes that were occurring in Greek comedy during the transitional period between the classical Hellenic period and the Hellenistic period ushered in by Alexander the Great and his inheriting Generals. Early (Old) Comedy morphed to New Comedy. The former was built on comparisons/contrasts/conflicts between the city-state (polis) and the house-hold or Family (oikos ). The former was morphed after 324 BC by the forces of the emerging nation-states (oikoumenê), entities built upon a more global fabric and economy (oikonomia). The analogy between pre-Web culture and today's Internet world is obvious. Old fashions must be subsumed. New Comedy turned away from parody of the failure of the city-state leadership, and focused on relationships among and between families, such as marriages, property, and social roles. This pathway led to Commedia dell'Arte and today's funny world.21Envision the new comedy of our anachronistic Web-challenged solon-driven copyright laws, facing the photocopier past, the Internet present, and a wired-world future. Or, the new comedy of an editorial board meeting this Spring where 75% of the members did not know what MP3 or Napster are, and how they have changed the dissemination of information forever. In music, the ostriches of RIAA, ASCAP and BMI shiver in the sand. Chemistry publishers need to be swift kangaroos.
A recent news release has announced a new chemistry e-preprint server located at ChemWeb.com (http://preprint.chemweb.com) that will accept any document about chemistry. "The preprints are to be submitted in standard word-processing formats. Additional supporting files or graphics can be included. Once posted, readers can comment on it, a nontraditional form of peer review. Authors will have the option of replacing the original submission with revised versions. Readers can access the preprints without fee, and sort through them using a variety of filtering mechanisms. Hot-articles with high hit-rates will be highlighted. Papers will be ranked by reader's evaluations."
Coda: Whatever happens, Aristophanes' final scene in Ostrich suggests how chemists should view e-preprints:
"As those in pow'r do resist,
The price goes up, volume goes down;
And ostriches create committees that sit and frown.
Scatter the Web, that is its will;
As costs drop down, volume goes up,
And kangaroos at profit's table sup.
But think of the best;
Imagine our two legged choruses mate,
Authors and readers would dance and elate."9
REFERENCES
1 Green, Peter, Armada from Athens, Hodder and Stoughton, London, 1971.
2 http://www.eff.org/~barlow/EconomyOfIdeas.html
3 This is an obvious outgrowth of a query by Strepsiades at Cloud 193,
"Why's their arse pointing up to the sky?"
and his guide's response:
"It's learning astronomy on its own!"
4 http://xxx.lanl.gov/
http://www-spires.slac.stanford.edu/FIND/spires.html
http://www-spires.slac.stanford.edu/find/hep
http://preprints.cern.ch/
http://www.ncstrl.org/
http://kerouac.pharm.uky.edu/ASRG/wave/wavehp.html
http://publish.aps.org/eprint/
5 http://elib.cs.berkeley.edu/tilebars/
6 From The Song of the Nightingale, Timberlake Wertenbaker, "Myths are oblique images of yearned for truths that echo across time"
8 Chemical and Engineering News, June 12, 2000, p8, "Letters", Jiri Janata.
9 Indented quotes are taken from the fragments of Ostrich, by Aristophanes, interpreted by RED.
Scansion is freely adapted because of rare technical words and damage to the manuscript.
10 Aristophanes was obviously deceived by conflicting reports of animals from Africa/Arabia, and elsewhere. The ostrich was known to the Classic Greeks, as were some marsupials — but not, obviously, the kangaroo. Until the rest of the MS is found, this allusion remains an enigma.
11 Chemical and Engineering News, June 5, 2000, p 15-16.
12 Aristophanes' reference to a "Web" is obscure. The root word used is arachne (araxnh). It may refer to a new way of distributing copies of his scripts.
13 http://www.stsci.edu/stsci/meetings/lisa3/hanischr.html
14 http://doright.stsci.edu/~payne/iau.97/
15 http://www.stsci.edu/stsci/meetings/lisa3/hanischr.html
16Nature 397, 199 (1999)
17 http://www.slac.stanford.edu/grp/tis/talks/keymgr-199912/tsld014.htm
18Clouds, Aristophanes
19 Nature 390, 427 (1997)
Science 273: 304 (1996) (Gary Taubes)
Science 271: 767 (1996) (Gary Taubes)
Science 271: 764 (1996) (Gary Taubes)
20 Nature 397, 195 - 200 (1999)
http://cas.bellarmine.edu/tietjen/images/writing_is_on_the_web_for_scienc.htm
21 The City as Comedy, Ed. Gregory Dobrov, UNC Press, Chapel Hill, NC, 1997