From owner-note@net.bio.net Fri Jan 01 22:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!uunet!utcsri!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <93002.085212FORSDYKE@QUCDN.QueensU.CA> Date: 2 Jan 93 13:52:12 GMT References: <92365.163145FORSDYKE@QUCDN.QueensU.CA> <1hvk5qINNe8e@agate.berkeley.edu> Organization: Queen's University at Kingston Lines: 52 In article Lazzaro (1992) Bnt.jrnl.note 1231, 2011 John Lazarro says: n Quote Forsdyke: >> The idea of privileged >>access to publication in a prestigious journal based on membership of some >>hierarchy seems to conflict with the proposed first article. PNAS is a - >collec >>tive platform for the scientific viewpoints of some senior scientists, but >not >>others. Sounds very un-American! >> Sincerely, Don Forsdyke (Discussion Leader) Lazzaro replies: >Then you must really hate edited books. Imagine, a publisher lets a >distinguished person (just one! not every distinguished person is the >entire field!) pick a group of authors based on the person's own >prejudicial choice of the best science in a field (imagine that! >making decisions based on personal taste!). Forsdyke's response: Here the publisher and the distinguished person he choses make their choices from the entire field of distinguished scientists, not the particular group of distinguished scientists who happen to be members of a particular club. Lazzaro continues: Scientific publications are all >about documentation, communication, and inspiration -- documents exist >to serve the readers, not the authors. Forsdyke replies: The readers are best served by unbiased access as possible to the best authors in the field, who should NOT be selected on the basis of race, religion, sex, creed, colour or membership of a particular club. >I am arguing for diversity -- science is much better served by a >plurality of "publication rules" than a single standard. Both >"strong-editor" and "weak-editor" publications should be allowed to >flourish, and PNAS is a specific example of a distributed >"strong-editor" format. Forsdyke replies: Being a "strong editor" means that you argue for diversity. You do not grant preferential authorship to members of a particular club, which has accepted as members certain distinguished scientists, but not others. Lazzaro continues: I resent making certain styles of >publications "illegal" -- censorship of form is just as pernicious as >censorship of content. Forsdyke replies: Censorship means deciding on the form and/or content of some form of publication, based NOT on the merits of the publication per se, but on the perception of what is "good" for the reader. Basing publication on what club the authors happen to belong to would seem to me a form of censorship Yours sincerely, Don Forsdyke. Discussion Leader. From owner-note@net.bio.net Fri Jan 01 22:00:00 1993 Path: biosci!agate!boom.CS.Berkeley.EDU!lazzaro From: lazzaro@boom.CS.Berkeley.EDU (John Lazzaro) Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <1i4pn9INNdjr@agate.berkeley.edu> Date: 2 Jan 93 19:16:57 GMT References: <92365.163145FORSDYKE@QUCDN.QueensU.CA> <1hvk5qINNe8e@agate.berkeley.edu> <93002.085212FORSDYKE@QUCDN.QueensU.CA> Organization: University of California, Berkeley Lines: 49 NNTP-Posting-Host: boom.cs.berkeley.edu In article <93002.085212FORSDYKE@QUCDN.QueensU.CA> writes: > >Here the publisher and the distinguished person he choses >make their choices from the entire field of distinguished >scientists, not the particular group of distinguished >scientists who happen to be members of a particular club. In an edited book, there is one (or a few) "distinguished persons" who are making their choices from the entire field of science. In PNAS, there are several hundred "distinguished persons" who are making their choices from the entire field of science. That is the only difference; in both cases, the editors are free to solicit or accept contributions from everyone. For your statement to be correct, PNAS would have to only publish contributions *authored* by the members. Your original problem with PNAS was that members said they had "promised" papers to other authors, or to their own lab, and thus were not interested in your publication. These members were classic "strong editors"; they wanted to express a point of view with their pages, and your research didn't serve that purpose. The members had the entire field to choose from, and chose the research they wanted to, and it didn't include yours. I see nothing discriminatory about this, this is the role of a strong editor. > >The readers are best served by unbiased access as possible to >the best authors in the field, who should NOT be selected on >the basis of [...] > You have no right to enforce your view of how a publisher's readers are best served; these views belong in a position paper, not in a enforced document. If I want to publish a journal that only accepts articles from female anthropologists, or department chairs, or scientists that are also creationists, I should be able to do this. A journal of this type will have a deep point of view, just as the National Review or The Nation has a deep point of view about US government and politics. > >Censorship means deciding on the form and/or content of >some form of publication, based NOT on the merits of the publication per se, >but on the perception of what is "good" for the reader. By definition, a "strong editor" makes content decisions for the good of the reader, this is the job of an editor. You are indeed promoting censorship, by telling PNAS (and every edited book published) how they are supposed to run their publication. From owner-note@net.bio.net Sun Jan 03 22:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!uunet!utcsri!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <93004.094133FORSDYKE@QUCDN.QueensU.CA> Date: 4 Jan 93 14:41:33 GMT References: <92365.163145FORSDYKE@QUCDN.QueensU.CA> Organization: Queen's University at Kingston Lines: 58 Regarding John Lazzaro's defence of the Proceedings of the National Academy of Sciences: This follows from the "Charter of Authors' Rights." proposed article 1. "1.Judgements concerning the acceptance, reviewing and publication of a paper should be concerned with the characteristics of the paper itself and not with the race, sex, creed or colour of the author."(Ref.2) David Kristofferson (ref.3) expanded on this, implying that the character- istics of the author might include his/her status in the heirarchy. If this were so, I then pointed out that the authorship discrimination practiced by the Proceedings of the National Academy of Sciences would aptly reflect the principle David was espousing. John Lazzaro then wrote arguing that PNAS is a special case (ref.1): In response to this I would point out that there are MANY very distinguished people in US science who are NOT members of the Academy. How is it that some distinguished scientists are in the club, but not others? Privileged access to publication in a prestigious journal based on membership of some heirarchy seems to conflict with the proposed first article. Lazzaro has since attempted to buttress his case with further arguments. While I accept the principle that making rules which cover every case is often not possible, I personally do not find Lazzaro's arguments that PNAS is a special case very convincing. The following note I received from someone whose anonymity I will respect, does not detract from my assessment of Lazzaro's case "The US. NAS is frequently in a state of embarassment when Nobel prizes are awarded to non-members. There have also been several cases where individuals declined membership since they "did science not politics." As a Canadian I am not in a position to check the validity of this assertion, but it does not sound too way out. Does anyone else have a view on this matter? Sincerely, Don Forsdyke. Discussion Leader. (1) Lazzaro, J. (1992) Bnt.jrnl.note 1228, 2324 (2) Forsdyke, D.R. (1992) Bnt.jrnl.note 1221, 1105 (3) Kristofferson, D. (1992) Bnt.jrnl.note 1222, 1631 (4) Forsdyke, D.R. (1992) Bnt.jrnl.note 1228, 1500 Sincerely, Don Forsdyke Discussion Leader (1) Forsdyke, D. R. (1992) Bionet.Journals.Note 1221, 1105 (2) Christoffersen, D. (1992) Bionet.Journals.Note 1222, 1631 (3) Baxter, A. (1992) Bionet.Journals.Note 1224, 750/ From owner-note@net.bio.net Sun Jan 03 22:00:00 1993 Path: biosci!agate!boom.CS.Berkeley.EDU!lazzaro From: lazzaro@boom.CS.Berkeley.EDU (John Lazzaro) Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <1ia36jINNg17@agate.berkeley.edu> Date: 4 Jan 93 19:29:23 GMT References: <92365.163145FORSDYKE@QUCDN.QueensU.CA> <93004.094133FORSDYKE@QUCDN.QueensU.CA> Organization: University of California, Berkeley Lines: 25 NNTP-Posting-Host: boom.cs.berkeley.edu In article <93004.094133FORSDYKE@QUCDN.QueensU.CA> writes: > > Lazzaro has since attempted to buttress his case with further arguments. >While I accept the principle that making rules which cover every case is often >not possible, I personally do not find Lazzaro's arguments that PNAS is a >special case very convincing. The following note I received from someone whose >anonymity I will respect, does not detract from my assessment of Lazzaro's case > >"The US. NAS is frequently in a state of embarassment when Nobel >prizes are awarded to non-members. There have also been several cases >where individuals declined membership since they "did science not >politics." > You are changing the focus of the discussion from the details of a policy, to rumour and innuendo. There is only one issue to resolve: Is PNAS any different from an edited book? I have made a convincing case that there is no difference, and you have chosen to ignore my arguments and turn to political issues. I have no interest in a discussion on that level. The specific case of PNAS is not the salient issue, the issue is the validity of the "edited book" journal format as an important form of scientific expression that should not be excluded by any policies. From owner-note@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!uunet!utcsri!helios.physics.utoronto.ca!alchemy.chem.utoronto.ca!mroussel From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel) Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <1993Jan5.144122.20725@alchemy.chem.utoronto.ca> Date: 5 Jan 93 14:41:22 GMT References: <93004.094133FORSDYKE@QUCDN.QueensU.CA> <1ia36jINNg17@agate.berkeley.edu> <93005.085026FORSDYKE@QUCDN.QueensU.CA> Organization: Department of Chemistry, University of Toronto Lines: 20 In article <93005.085026FORSDYKE@QUCDN.QueensU.CA> writes: >Lassaro says: >>Is PNAS any different from an edited book? > >Yes it is different, because journals are not edited books >and we are discussing journals. The "edited book" argument strikes me as being a little weak (PNAS is clearly not a book, as Forsdyke points out), but isn't the title of this particular periodical (PROCEEDINGS of the NAS) a warning that this is not a regular journal? When a scholarly society operates a real journal, it usually labels it clearly as such (for instance, Journal of the American Chemical Society) but when the publication in question is labeled "Proceedings" or "Transactions", I usually assume the sort of clubbish publication rules which apply to PNAS. (I realize that there are exceptions.) Doesn't everyone? Marc R. Roussel mroussel@alchemy.chem.utoronto.ca From owner-note@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!agate!ames!saimiri.primate.wisc.edu!zaphod.mps.ohio-state.edu!caen!uunet!utcsri!skule.ecf!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <93005.085026FORSDYKE@QUCDN.QueensU.CA> Date: 5 Jan 93 13:50:26 GMT References: <92365.163145FORSDYKE@QUCDN.QueensU.CA> <93004.094133FORSDYKE@QUCDN.QueensU.CA> <1ia36jINNg17@agate.berkeley.edu> Organization: Queen's University at Kingston Lines: 11 Lassaro says: >You are changing the focus of the discussion from the details of a policy, to >rumour and innuendo. There is only one issue to resolve: > >Is PNAS any different from an edited book? Forsdyke replies: Yes it is different, because journals are not edited books and we are discussing journals. But considering books, if I were asked to edit a book I would approach potential contributors based solely on their expertise not on whether they happened to be members of a certain club, access to which is rumoured to be rather politicised. From owner-note@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: vioque@cica.es (Agustin Vioque) Newsgroups: bionet.journals.note Subject: subscribe Message-ID: <1993Jan5.091110.19948@gserv1.dl.ac.uk> Date: 5 Jan 93 09:11:41 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 Content-Identifier: 90 Original-To: jrnlnote@uk.ac.daresbury (Receipt Notification Requested) (Non Receipt Notification Requested) Conversion: Prohibited subscribe From owner-note@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!agate!ames!think.com!hsdndev!husc-news.harvard.edu!husc.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: Date: 5 Jan 93 16:07:51 GMT References: <92365.163145FORSDYKE@QUCDN.QueensU.CA><93004.094133FORSDYKE@QUCDN.QueensU.CA> <1ia36jINNg17@agate.berkeley.edu> <93005.085026FORSDYKE@QUCDN.QueensU.CA> Lines: 20 Nntp-Posting-Host: husc10.harvard.edu Just a reminder of what PNAS stands for: Proceedings of the National Academy of Sciences It is rather silly to tell any organization how to run their (bi-)monthly newsletter. Originally, these "Proceedings" journals really were compilations of what was said at each society's meetings, but of course these papers aren't really "read" out loud anymore. Would PNAS be a better journal if it quit being the P of the NAS? Undoubtedly, since a great amount of junk and crockery gets published there. But it's their right to operate in such an idiosyncratic manner if they so choose. Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-note@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!agate!boom.CS.Berkeley.EDU!lazzaro From: lazzaro@boom.CS.Berkeley.EDU (John Lazzaro) Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <1icl2oINN7dh@agate.berkeley.edu> Date: 5 Jan 93 18:46:48 GMT References: <1ia36jINNg17@agate.berkeley.edu> <93005.085026FORSDYKE@QUCDN.QueensU.CA> Organization: University of California, Berkeley Lines: 21 NNTP-Posting-Host: boom.cs.berkeley.edu > (Marc R. Roussel) writes: >[..] but isn't the title of this particular periodical (PROCEEDINGS of >the NAS) a warning that this is not a regular journal? [ ..] > (Keith Robison) writes: >Just a reminder of what PNAS stands for: > Proceedings of the National Academy of Sciences > It is rather silly to tell any organization how to run their (bi-)monthly >newsletter. [..] It's their right to operate in such an idiosyncratic manner if >they so choose. Exactly, there is freedom of the press in this country, and it extends to scientific journals. My points have nothing to do with the proported political nature of PNAS. I am simply protesting an attempt to place restrictions on the freedom to publish. If people don't like PNAS or any other publication, don't read it, petition your library to unsuscribe, petition you colleagues to submit elsewhere, but don't try to enforce rules and regulations on publishers and editors. From owner-note@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!CSHL.ORG!anderson From: anderson@CSHL.ORG (John Anderson) Newsgroups: bionet.journals.note Subject: UNsubscribe me from jrnlnote Message-ID: <9301051844.AA20745@xray1.cshl.org> Date: 5 Jan 93 18:44:11 GMT References: <9301051832.AA19150@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 7 Please unsubscribe me from bionet.journals.note. Thanks ------- John E. Anderson W. M. Keck Structural Biology Laboratory Cold Spring Harbor Laboratory From owner-note@net.bio.net Mon Jan 04 22:00:00 1993 Path: biosci!agate!boom.CS.Berkeley.EDU!lazzaro From: lazzaro@boom.CS.Berkeley.EDU (John Lazzaro) Newsgroups: bionet.journals.note Subject: Re: In defense of PNAS Message-ID: <1ick7eINN78u@agate.berkeley.edu> Date: 5 Jan 93 18:32:14 GMT References: <93004.094133FORSDYKE@QUCDN.QueensU.CA> <1ia36jINNg17@agate.berkeley.edu> <93005.085026FORSDYKE@QUCDN.QueensU.CA> Organization: University of California, Berkeley Lines: 8 NNTP-Posting-Host: boom.cs.berkeley.edu In article <93005.085026FORSDYKE@QUCDN.QueensU.CA> writes: >But considering books, if I were asked to edit >a book I would approach potential contributors based solely on their expertise >not on whether they happened to be members of a certain club [../ Once again, you have the analogy wrong. The only member of the club in this case is you, the chosen editor, who can choose any person you want. From owner-note@net.bio.net Wed Jan 06 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!zaphod.mps.ohio-state.edu!caen!uunet!utcsri!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Is PNAS a special case? Message-ID: <93007.163339FORSDYKE@QUCDN.QueensU.CA> Date: 7 Jan 93 21:33:39 GMT Organization: Queen's University at Kingston Lines: 23 ======================================================================== 32 In article , robison1@husc10.harvard.edu (Keith Robison) says: > > It is rather silly to tell any organization how to run their (bi-)monthly >newsletter. Forsdyke: No one is trying to do that. The issue is whether PNAS is a special case to be regarded as an exception even though it appears to violate Article 1 of a proposed Charter of Authors' Rights. > Would PNAS be a better journal if it quit being the P of the NAS? >Undoubtedly, since a great amount of junk and crockery gets published there. >But it's their right to operate in such an idiosyncratic manner if >they so choose. > A charter of Editors' Rights might postulate the right to operate idiosyncratically. Here there would be a conflict between Author's Rights and Editor's rights! Note that the FIRST "proceedings", the Proceedings of the Royal Society, which began in the 17th century, does not, I believe, demonstrate this idiosyncrasy. Don Forsdyke From owner-note@net.bio.net Sun Jan 10 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!psuvax1!psuvm!mek104 From: MEK104@psuvm.psu.edu Newsgroups: bionet.journals.note Subject: subscription info wanted Message-ID: <93011.162850MEK104@psuvm.psu.edu> Date: 11 Jan 93 21:28:50 GMT Organization: Penn State University Lines: 11 A colleague of mine would like the address to subcribe to Bionet.journals.note. If anyone has it, I would appreciate you sending it along to me. Penn State provides this network for all account holders so I've never had to subscribe. thanks again, Mark Kubiske < MEK104@PSUVM.PSU.EDU > School of Forest Resources Penn State University From owner-note@net.bio.net Wed Jan 13 22:00:00 1993 Path: biosci!agate!spool.mu.edu!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: List of topics Message-ID: <93014.101017FORSDYKE@QUCDN.QueensU.CA> Date: 14 Jan 93 15:10:17 GMT Organization: Queen's University at Kingston Lines: 48 The original charter of this group included the following list of topics. POSSIBLE TOPICS How does an Editor select a reviewer? How many reviewers for a paper? One, two, three..? Should papers be transmitted by courier or regular post? Anonymous reviewing? Which journals are likely to be receptive of "way out" ideas? Which journals are prone to defend the conventional wisdom? Does the annual Impact Rating influence an Editor's choice of manuscripts Is submitting a paper to Nature/Science a waste of time when so few papers can be published? Salami publishing? Honorary authorship (Fabrikant and all that)? Should a technician be a coauthor or be mentioned in acknowledgements? What is a reasonable time for a reviewer to retain a paper? Electronic publishing? How should the paper media cite items in the electronic media? Do editors of the paper media feel threatened by the electronic revolution? Should they? Peer review. Publish or perish? Order of authors' names on a paper? Should reviewers be paid? Does any journal in the biomedical sciences pay authors? Science writing and literary style? When should a finding be described as "novel"? Since many readers do not have English as a first language, should papers in English take this into account? Should all scientific writing be in English? Double publishing,...of papers?...of abstracts? Equal sins? Priority and credit. Fraud and plagiarism. Page charges. Confidentiality of reviewing. Do editors deliberately slow manuscript handling to give authors more time to reconsider? Better to submit to a non-profit journal (e.g. Biochem.J., BioEssays)? Do Editors retain unique formats (e.g. citation by author rather than by number) to make it more difficult for authors to revise manuscripts for submission elsewhere? What are the "rights" of an author? Sincerely, Don Forsdyke Department of Biochemistry, Queen's University, Kingston, Canada K7L3N6 forsdyke@qucdn.queensu.ca From owner-note@net.bio.net Wed Jan 13 22:00:00 1993 Path: biosci!agate!spool.mu.edu!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Editors should edit Message-ID: <93014.101452FORSDYKE@QUCDN.QueensU.CA> Date: 14 Jan 93 15:14:52 GMT Organization: Queen's University at Kingston Lines: 25 Editors should Edit. THE DEGENERATION OF ENGLISH "Paradigm"..................."Novel" Language has to move on, and few would mourn the passing on of the term "allelomorph" which characterized the early genetics literature of the 20th century, and its replacement with "allele". However, editors have a responsibility to check papers for usages which clearly represent a degeneration of English. I am noting quite often the use of the term "paradigm", meaning simply "model". As far as I am aware "paradigm" was introduced by Thomas Kuhn to mean a large conceptual frame-shift. Thus, Burnet's clonal selection theory presented a new paradigm which revolut- ionized the way immunologists think about their subject. Recently in Nature there was some discussion of the misuse of the term "novel", not just as an alternate for "new", but meaning especially, superlatively, new,.....almost in a paradigmatic sense. I think editors have a responsibility here to point this out to authors, particularly those who use "novel" in the title. At the very least, the work should be unchallengeably novel and imply a quite exhaustive literature search to check that the finding really is new. Sincerely, Don Forsdyke From owner-note@net.bio.net Wed Jan 13 22:00:00 1993 Path: biosci!agate!spool.mu.edu!yale.edu!jvnc.net!tigger.jvnc.net!sandy From: sandy@nmr1.pt.cyanamid.COM (Sandy Silverman) Newsgroups: bionet.journals.note Subject: Re: Editors should edit Message-ID: Date: 14 Jan 93 21:48:33 GMT References: <93014.101452FORSDYKE@QUCDN.QueensU.CA> Sender: news@tigger.jvnc.net (Zee News Genie) Organization: American Cyanamid Company Lines: 10 In-Reply-To: 's message of Thu, 14 Jan 1993 10:14:52 EST Nntp-Posting-Host: nmr1.pt.cyanamid.com I can't resist mentioning a couple of pet peeves of my own: A gene "codes for" or "encodes" but doesn't do both at the same time (unless it encodes more than one polypeptide, but let's not get too picky!) rDNA originally referred to ribosomal DNA and, I think, still should. What should the acronym for recombinant DNA be? -- Sanford Silverman >Opinions expressed here are my own< American Cyanamid sandy@pt.cyanamid.com, silvermans@pt.cyanamid.com "Yeast is Best" From owner-note@net.bio.net Thu Jan 14 22:00:00 1993 Path: biosci!agate!ames!saimiri.primate.wisc.edu!caen!uwm.edu!psuvax1!psuvm!pqq From: PQQ@psuvm.psu.edu Newsgroups: bionet.journals.note Subject: Re: Editors should edit Message-ID: <93015.132546PQQ@psuvm.psu.edu> Date: 15 Jan 93 18:25:46 GMT References: <93014.101452FORSDYKE@QUCDN.QueensU.CA> Organization: Penn State University Lines: 13 I agree editors should edit assuming they are literate, not simply good scientists. Most editing flaws could be chalked up to copy editors who are also supposed to know the language. So let's try to teach and exemplify what a former professor called "telescopic writing" in which no more words or letters are used than are needed. In addition to saying "model" (not paradigm), we should also reject a few neologisms like the neoverb "to electrophorese" of (heaven forbid) "to PCR". I'd love to build a list of the most hated, misused "terms." Dick Pratt BITNET:pqq@psuvm INTERNET: pqq@psuvm.psu.edu 7 Ferguson Bldg. Penn State University Park, PA 16802 814/865-6942 From owner-note@net.bio.net Thu Jan 14 22:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!uunet!math.fu-berlin.de!unidui!rrz.uni-koeln.de!rrz.uni-koeln.de!biomed.biolan.uni-koeln.de!KHOFMANN From: khofmann@biomed.biolan.uni-koeln.de Newsgroups: bionet.journals.note Subject: quotation of database entries, software etc. Message-ID: <1993Jan15.082431.128588@rrz.uni-koeln.de> Date: 15 Jan 93 08:24:31 GMT Sender: news@rrz.uni-koeln.de (Usenet News System) Reply-To: khofmann@biomed.biolan.uni-koeln.de Organization: Biochemical Institute, Cologne University Lines: 41 Perhaps this is a little bit off the topic, but i have been considering the following problems for quite a time now: 1. Teh first problem will be known to a big number of sequencing scientists: Suppose you published a sequence in a database as GENBANK or EMBL. I have the impression that one could as well publish it in a wastebasket unless you have an paper on this sequence published in a 'real' journal. By reading all those seqeunce-containing papers in even the most prestigeous journals you get the feeling that the authors do check the databases for similar or identical proteins or DNA. Everyone writes something like: 'A search of available DNA data bases revealed no significant homology...' or 'A search of GENBANK rel. XX revealed this and that...' But you mostly read such phrases if nothing was found with the database searches. But what do authors do, if somebody else has in fact cloned a similar/identical cDNA/gene? If it has been published on paper, one usually doesn't get around citing it. But if it is onlyin some database, there are many workarounds: Besides the old trick of searching outdated databases, here are some more elaborate ways - 'A search of current sequence databases revealed no significant homology to previously published sequences' - 'Databae searches indicate that this protein is not homologeous to any identified protein of mammalian origin' (Nature) (forget about this 80% identical rat protein with only putative function) - 'A search of DNA databases revealed no overall similarity to previously identified sequences' (better not check PIR/SwissProt, might find something there..) But seriously, are there some guidelines of how to assure that authors 1) have checked appropriate and current databases 2) mention it if they found something And, how should sequence data base entries be cited anyway? Since sequencing is becoming kind of trivial these days and many journals discourage publishing papers with focus on sequencing, publishing sequences in a database ought to be encouraged. But I will not be in favour of this approach as long as nobody feels the need of even mentioning your work. With best regards, Kay Hofmann From owner-note@net.bio.net Sun Jan 17 22:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!uunet!spool.mu.edu!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: <93018.121123FORSDYKE@QUCDN.QueensU.CA> Date: 18 Jan 93 17:11:23 GMT References: <1993Jan15.082431.128588@rrz.uni-koeln.de> Organization: Queen's University at Kingston Lines: 38 Kay Hoffman writes: >1. The first problem will be known to a big number of sequencing scientists: >Suppose you published a sequence in a database as GENBANK or EMBL. I have >the impression that one could as well publish it in a wastebasket unless >you have an paper on this sequence published in a 'real' journal. This is part of the general problem of getting the paper media to acknowledge the electronic media, by appropriate citations. This would be considerably helped if we could agree on an appropiate way of citating an electronic publication. I have suggested that each day be considered to constitute a "volume" and each second be considered a page. Thus this communication is "Forsdyke, D. R. (1993) Bnet.jrnl.note 118, 1211est" >But seriously, are there some guidelines of how to assure that authors >1) have checked appropriate and current databases >2) mention it if they found something If they have not done this, then others may point it out in the letter columns of the journal or (even) on this medium. This would be a valid role for Bionet.Journals.Note. >Since sequencing is becoming kind of trivial these days and many journals >discourage publishing papers with focus on sequencing, publishing sequences >in a database ought to be encouraged. But I will not be in favour of this >approach as long as nobody feels the need of even mentioning your work. The following quote from the Editor of DNA Sequence may assuage some of your doubts: "I detect an ignorance of how much information there may be in a DNA sequence and possibly a prejudice against DNA sequencing as being some kind of unintellectual pursuit. Sequencing can be a long an onorous task, but the end result of a carefully determined and carefully analysed sequence can be a wealth of new information and insight." Bart Barrell Sincerely, Don Forsdyke (Discussion Leader) From owner-note@net.bio.net Sun Jan 17 22:00:00 1993 Path: biosci!ucselx!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!news.acns.nwu.edu!network.ucsd.edu!riscsm!usenet From: bashford@scripps.edu (Don &) Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: Date: 18 Jan 93 22:36:42 GMT References: <1993Jan15.082431.128588@rrz.uni-koeln.de> <93018.121123FORSDYKE@QUCDN.QueensU.CA> Sender: usenet@riscsm.scripps.edu Organization: The Scripps Research Institute, La Jolla, CA, USA Lines: 13 In-Reply-To: 's message of Mon, 18 Jan 1993 12:11:23 EST >>>>> In article <93018.121123FORSDYKE@QUCDN.QueensU.CA>, writes: DF> Thus this communication is "Forsdyke, D. R. (1993) Bnet.jrnl.note DF> 118, 1211est" Except that on my machine your post is number 43, not 118. Article numbers vary according to the order in which messages arrive in different places and so are no good as identifiers. However, UseNet news does supply a Message-ID field in the header (your message was <93018.121123FORSDYKE@QUCDN.QueensU.CA> But what about mailing list propagation? Does it supply the same ID? Don Bashford From owner-note@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!agate!spool.mu.edu!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: <93019.093722FORSDYKE@QUCDN.QueensU.CA> Date: 19 Jan 93 14:37:22 GMT References: <1993Jan15.082431.128588@rrz.uni-koeln.de> <93018.121123FORSDYKE@QUCDN.QueensU.CA> Organization: Queen's University at Kingston Lines: 18 In article , bashford@scripps.edu (Don &) says: > >>>>>> In article <93018.121123FORSDYKE@QUCDN.QueensU.CA>, > writes: > >DF> Thus this communication is "Forsdyke, D. R. (1993) Bnet.jrnl.note >DF> 118, 1211est" > >Except that on my machine your post is number 43, not 118. Article >Don Bashford The 118 is the "volume" number, with one day composing a volume. "118" means the first month of the year ("1") and the eighteenth day of that month ("18"). Thus each item can be categorized based on time of submission. Sincerely, Don Forsdyke From owner-note@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.journals.note Subject: BIOSCI/bionet Frequently Asked Questions Message-ID: <9301191000.AA25327@net.bio.net> Date: 19 Jan 93 10:00:02 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 16 New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-note@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!yale.edu!not-for-mail From: smith-una@yale.edu (Una Smith) Newsgroups: bionet.general,bionet.journals.note Subject: Editorial license in bionet Message-ID: <1jg2r3INNfrq@MINERVA.CIS.YALE.EDU> Date: 19 Jan 93 05:16:19 GMT Organization: Yale University Science & Engineering UNIX(tm), New Haven, CT 06520-2158 Lines: 56 Xref: biosci bionet.general:3874 bionet.journals.note:46 NNTP-Posting-Host: minerva.cis.yale.edu In "BIOSCI FAQs will be changed", bionet.announce, 13 January 1993, David Kristofferson wrote: "BIOSCI/bionet will no longer be distributing the FAQ composed by Una Smith at her request (BIOSCI FAQ I)." I objected when the article "Bionet (BIOSCI) FAQ I" appeared two weeks ago in bionet.announce, under my name. It was not posted by me. David and I had discussed making my FAQ a periodic posting together with his own regularly posted documents. During the holidays he informed me of his plan to distribute an edited version of my FAQ. I responded that I would consider adding his changes to the current version of the FAQ when I returned from vacation, but that I did not want him to distribute it. David replied that it would be more convenient for him to distribute the FAQ as he had indicated he would. When David did not get a prompt reply from me (I was away), he assumed that I consented to his plan. David changed most instances of the word "Bionet" in my FAQ to "BIOSCI". He and I have argued publicly over whether these are equivalent. I argue that there is an important difference, which revolves around whether the "BIOSCI/bionet" hybrid that David and we have created will grow according to the conventions of "owned" mailing lists or "public" Usenet newsgroups. David's motives in arguing for strict ownership are good: he is concerned that if he does not exert control, the professional quality of the bionet groups will deteriorate. I appreciate David's custodianship of the mailing lists, and I approve of most of what he has done, but I think the bionet newsgroups would be even better if they were less tightly controlled. Our argument has apparently made David feel the need to declare himself "editor", then edit and post my FAQ. See David's own FAQ, "Consolidated BIOSCI/bionet FAQ" (bionet.announce, 18 January 1993), where he writes: "BIOSCI messages are distributed without editorial intervention in most cases." After the list of newsgroup names, he adds: "** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup." As far as I know, I am the first person to whom this editorial policy has been applied. It goes far beyond the occasional insertion of [bracketed] comments at the top of articles. In effect, David has tried to "resolve" our argument by putting his own words in my mouth. This is a violation of my rights as an author and David's authority as a moderator. It made me very angry, and I sent David e-mail demanding an apology in a tone designed to frustrate and anger him, for which I now publicly apologize. Two wrongs don't make a right, only a fight. I am sorry. -- Una Smith Biology Department smith-una@yale.edu Yale University New Haven, CT 06511 From owner-note@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!agate!ames!elroy.jpl.nasa.gov!sdd.hp.com!cs.utexas.edu!uunet!mcsun!news.funet.fi!hydra!klaava!saarikko From: saarikko@klaava.Helsinki.FI (Jarmo Saarikko) Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: <1993Jan19.152237.28557@klaava.Helsinki.FI> Date: 19 Jan 93 15:22:37 GMT References: Organization: University of Helsinki Lines: 33 X-Newsreader: TIN [version 1.1 PL6] > "Forsdyke, D. R. (1993) Bnet.jrnl.note 118, 1211est" > Except that on my machine your post is number 43, not 118. > However, UseNet news does supply a Message-ID field in the header (your > message was <93018.121123FORSDYKE@QUCDN.QueensU.CA> But what about > mailing list propagation? Does it supply the same ID? Dear Don, it seems that quite many of us (including me) do not understand Forsdyke's reference type. I had to ask him this about a month ago. I think he hasn't replied to you yet, so I will do it publicly: The year of writing is in the parentheses, 118 should perhaps read 0118, which stands for January 18th and 1211est is the local time when he sent the message. If you read the Message-ID header you find the same information there! I received the same header, Forsdyke has only spelled it out, leaving the sender's address out. In my opinion the newsgroup name should be the original whole name and should not be abbreviated. It then remains to be explained how a message on a mailing list (not linked to newsgroups) should be referred to? There is probably a message-ID created by the sender's mailer-software, but it may have nothing to do with the time of sending by the software/noed of the mailing-list, which is to be preferred. Perhaps Don Forsdyke has a proposal? Jarmo Saarikko # Jarmo.Saarikko@Helsinki.FI # Voice: +358-0-1917415 (GMT+2h) # # SAARIKKO@FINUH.BITNET # Fax: +358-0-1917492 # # Department of Zoology, Division of Ecology, (Pohjoinen Rautatiekatu 13) # # P.O. BOX 17, SF-00014 UNIVERSITY OF HELSINKI, Finland # From owner-note@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!agate!spool.mu.edu!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: <93019.165125FORSDYKE@QUCDN.QueensU.CA> Date: 19 Jan 93 21:51:25 GMT References: <1993Jan15.082431.128588@rrz.uni-koeln.de> Organization: Queen's University at Kingston Lines: 8 My basic point is that in order to link up the citing system of the electronic media to the paper media, we need to adopt a style which the paper people will understand. On solution to this is to use each day as a "volume", and each second as a "page". Sometime, there has to be some meeting of Editors of paper and electronic media to hammer out some solution. Sincerely, Don Forsdyke From owner-note@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!chipmunk.bio.indiana.edu!gilbertd From: gilbertd@chipmunk.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: Date: 19 Jan 93 18:29:56 GMT References: <93018.121123FORSDYKE@QUCDN.QueensU.CA>> Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 43 Nntp-Posting-Host: chipmunk.bio.indiana.edu >I am not sure if you can search for either Message id or date and time >by Gopher, so it seems rather tedious to dig out an old article... You CAN search for the Usenet message ID of any bionet news article thru Gopher to the IUBio news archive. You will not only get the original message, but all entries which reference that message (i.e., all follow ups). Here is an example (use quote marks for a literal search): Bionet News at IUBio archive: '92231.161618FORSDYKE@QUCDN.QueensU.CA' 1. shiv@tsp.m Re: Re: Journal Watch: MHC and intracellular self. 2. 6. > -- Don -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-note@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!agate!spool.mu.edu!yale.edu!ira.uka.de!news.belwue.de!news.uni-tuebingen.de!studserv!zxmkr08 From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: Date: 19 Jan 93 16:42:23 GMT References: <1993Jan15.082431.128588@rrz.uni-koeln.de> <93018.121123FORSDYKE@QUCDN.QueensU.CA> Sender: news@softserv.zdv.uni-tuebingen.de (News Operator) Organization: Comp. Center (ZDV) U of Tuebingen, FRG Lines: 26 In bashford@scripps.edu (Don &) writes: >>>>>> In article <93018.121123FORSDYKE@QUCDN.QueensU.CA>, writes: >DF> Thus this communication is "Forsdyke, D. R. (1993) Bnet.jrnl.note >DF> 118, 1211est" >Except that on my machine your post is number 43, not 118. Article >numbers vary according to the order in which messages arrive in >different places and so are no good as identifiers. However, UseNet >news does supply a Message-ID field in the header (your message >was <93018.121123FORSDYKE@QUCDN.QueensU.CA> But what about mailing >list propagation? Does it supply the same ID? I think 118 stands for Jan 18th which is the date when Don wrote his message; 1211est seems to be the time. I am not sure about ids, though; I am not sure if you can search for either Message id or date and time by Gopher, so it seems rather tedious to dig out an old article... (At least it is tedious for me since our connections are soooo slow :-( ) >Don Bashford -- /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ /* email: krasel@studserv.zdv.uni-tuebingen.de (Internet) HAS CHANGED!! */ /* NO WIN/X400 MAIL POSSIBLE AT THE MOMENT! */ /* "People are DNA's way of making more DNA." (R. Dawkins / anonymous) */ From owner-note@net.bio.net Tue Jan 19 22:00:00 1993 Path: biosci!agate!ames!haven.umd.edu!uunet!spool.mu.edu!enterpoop.mit.edu!bloom-picayune.mit.edu!athena.mit.edu!retentiv From: retentiv@athena.mit.edu (Sandra Chang) Newsgroups: bionet.journals.note Subject: Science Message-ID: <1993Jan20.032833.1014@athena.mit.edu> Date: 20 Jan 93 03:28:33 GMT Sender: news@athena.mit.edu (News system) Organization: Massachusetts Institute of Technology Lines: 10 Nntp-Posting-Host: vongole.mit.edu Hi. I'm a staff reporter with Science (And as such, I have no input into or knowledge of manuscript selection--so don't flame me!). I'm curious whether it would be helpful to this forum to have someone from our editorial side answering queries of a general nature. I make no promises and may be sticking my nexk out to far. But if there is interest, I could inquire. john travis ne bureau (please respond to jstravis@world.std.com "retentiv" is a friends account!) From owner-note@net.bio.net Tue Jan 19 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.journals.note Subject: Re: quotation of database entries, software etc. Message-ID: Date: 20 Jan 93 06:21:43 GMT References: <1993Jan15.082431.128588@rrz.uni-koeln.de> <93019.165125FORSDYKE@QUCDN.QueensU.CA> Organization: BIOSCI International Newsgroups for Biology Lines: 51 Every time this debate comes up, I drag out this old posting which I still like myself. Don Gilbert is right that the Message-Id is probably the most definitive and potentially useful feature in a message, but I doubt if it will win widespread following in the user community due to its apparent complexity. His example of its use with Gopher was convincing though (so I should modify my earlier opinion below 8-). In regards to another question, message ids are supposed to be unique, and I do not believe that they are affected by going from mail to news or vice versa (though I am not going to swear by this given the multitude of programs in existence 8-). Dave ---------------------------------------------------------------------- From bionet.general Thu May 7 18:11:45 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.general Subject: Citing BIOSCI/bionet postings Message-ID: Date: 18 Dec 91 00:41:52 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 27 Donald, If one wanted to cite a posting I would suggest a format which includes the name and e-mail address of the person posting the message, the Subject: line of the message, the newsgroup name, and the date/time stamp. If one really wants to become fanatical, note that each message has a unique message id line. (yours was: Message-Id: <9112171614.AA22659@genbank.bio.net> ) This latter info is not much use to humans though. I would not advocate using article numbers from your newsreader because this varies from site to site. An example reference for your posting would thus be: Forsdyke, Donald R. (FORSDYKE@QUCDN.QueensU.CA), "Reorganization: implication for electronic journal." USENET/bionet.general, 17 Dec 91 15:48:09 GMT. Hope this helps. Just writing it down in that format gives it a bit more authority, doesn't it 8-)?! One could also potentially have priority fights get down to the second, too (what fun). Dave From owner-note@net.bio.net Wed Jan 20 22:00:00 1993 Path: biosci!agate!spool.mu.edu!sdd.hp.com!swrinde!zaphod.mps.ohio-state.edu!sol.ctr.columbia.edu!The-Star.honeywell.com!umn.edu!lynx.unm.edu!carina.unm.edu!bhjelle From: bhjelle@carina.unm.edu Newsgroups: bionet.journals.note Subject: Re: Science Message-ID: <1jmclvINNs2g@lynx.unm.edu> Date: 21 Jan 93 14:41:03 GMT References: <1993Jan20.032833.1014@athena.mit.edu> Organization: University of New Mexico, Albuquerque Lines: 15 NNTP-Posting-Host: carina.unm.edu In article <1993Jan20.032833.1014@athena.mit.edu> retentiv@athena.mit.edu (Sandra Chang) writes: > >Hi. I'm a staff reporter with Science (And as such, I have no input into >or knowledge of manuscript selection--so don't flame me!). I'm curious >whether it would be helpful to this forum to have someone from our editorial >side answering queries of a general nature. I make no promises and may >be sticking my nexk out to far. But if there is interest, I could inquire. > >john travis >ne bureau Sounds great! What particular type of questions would you be willing to entertain? Brian From owner-note@net.bio.net Thu Jan 21 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.journals.note Subject: Re: Science Message-ID: Date: 22 Jan 93 00:56:25 GMT References: <1993Jan20.032833.1014@athena.mit.edu> Organization: BIOSCI International Newsgroups for Biology Lines: 22 retentiv@athena.mit.edu (Sandra Chang) writes: >Hi. I'm a staff reporter with Science (And as such, I have no input into >or knowledge of manuscript selection--so don't flame me!). I'm curious >whether it would be helpful to this forum to have someone from our editorial >side answering queries of a general nature. I make no promises and may >be sticking my nexk out to far. But if there is interest, I could inquire. >john travis >ne bureau >(please respond to jstravis@world.std.com "retentiv" is a friends account!) DEFINITELY!! I would hope that other journals would also get involved! Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net