More GBIF questions (was: ITIS)

B.J.Tindall bti at DSMZ.DE
Fri Jun 25 08:27:57 CDT 2004

Dear Tom, Neal, Doug, and Rich,
... small voice in the corner (as usual), both bacteriology and virology
have already experimented with and implemented what is being discussed
here. As I seem to keep pointing out, despite the fact that the system is
clearly defined the majority of end users get it wrong, and unfortunately
most of the providers of data...... There is a difference between keeping
your finger on the pulse and opening up the jugular!
Okay I will keep quiet - again......

At 16:13 24.6.2004 -0700, Doug Yanega wrote:
>Tom Lammers wrote:
>>At 02:41 PM 6/24/04, Neal Evenhuis wrote:
>>>This does not mean we allow taxonomists to dictate the Code (Tom's
>>>"wagging the dog" bit above).
>>My point was that it should not be modified for ad hoc purposes, for the
>>convenience of a single user-group, but rather on the basis of what is best
>>for science as a whole.  Modifying the Code to accommodate "informatics"
>>types is putting the cart before the horse: the informatics types should
>>modify THEIR procedures to bring them in line with what taxonomists do and
>>have done for years.
>Like insisting that only paper publication of names is viable, and
>tolerating non-reviewed publications? Certain traditions are
>worthwhile, and others are problematic. The Code-mandated reliance
>upon traditional print media is a hindrance to the efficient and
>timely compilation and dissemination of taxonomic information. That's
>not simply one user group that benefits if the Codes are changed,
>it's ALL user groups, AND the taxonomists themselves (i.e., "science
>as a whole").
>Wouldn't it be useful to everyone if every taxonomic publication in
>existence could be found on a single website? Wouldn't it be useful
>to taxonomists if they no longer had to worry about things like
>turnaround times, or page charges, or additional costs if they want
>to use high-resolution, full-color digital images in their works?
>That's the kind of thing I had in mind when I suggested the Codes
>might need to change to better reflect our times. Opening the door to
>digital publication also allows for other significant changes, such
>as regarding the following:
>Meredith Lane wrote:
>>While the means to do this is not yet a reality and it will take some
time to
>>put it in place, you can bet that such a means will be easier (and
>>much faster,
>>given the antipathy that taxonomists in general have toward agreeing with
>>another---I will brook no argument here; there is too much empirical
>>for this right here on Taxacom) than developing a "consensus taxonomy"
>>the whole of life.  Am I arguing that we should not strive for such a
>>consensus? Of course not. It's just that it is much harder to see that
>>happening than it is to imagine GBIF's goals achieved through flexible IT
>>developments based on accepted standards for data and metadata, and
>>mappings to
>>ontologies that can grow and evolve.  The only way that information
>>systems that
>>are truly helpful to science and society will become truly useful is if they
>>come to encompass the flexibility, contentiousness, and ability to encompass
>>more than one opinion at the same time that our own brains have --
>>forcing such
>>systems to "consensus" (not to say uniformity) will stifle true progress.
>>If we wait for a consensus in taxonomic opinion, biodiversity is going to be
>>long gone (we all know this is true: just witness the years and years
worth of
>>arguments on Taxacom about species concepts that show no sign of reaching a
>>conclusion, much less a consensus!), and so that consensus opinion will not
>>matter one iota.
>I fully understand your objection, but still believe that if the
>system is properly constructed, we *can* attain a functional
>consensus without any delays (i.e., no "waiting"), and without
>stifling progress. Consider a hypothetical example based on the
>status quo: taxonomist A, one of only two living experts on a certain
>group, publishes a paper in journal X, after it is seen by 3 peer
>reviewers and takes 9 months from submission to publication. Two
>months later, taxonomist B (who had been explicitly avoided as a peer
>reviewer at A's insistence) reads it, disagrees, and after 9 more
>months, publishes another paper in journal Y (which he personally
>edits, so there's no chance of rejection), and the two papers differ
>in several respects of classification. Some people will simply use
>whichever is more recent, some people will only see one (by chance)
>and use that one by default, some people will read both and choose
>one, some people will derive their own hybrid scheme using elements
>of both, etc., etc. - but the point is that the vast majority of
>users will never interact with other users when making their
>decision, nor will they interact with the authors of the papers in
>question, nor will the authors interact with one another in a
>constructive fashion.
>Now consider the type of system I'm proposing: taxonomist A puts up a
>draft manuscript onto the global taxonomy website, and every
>subscriber in the world who has flagged that as a taxon of interest
>is instantly notified (including taxonomist B). Taxonomist B puts up
>a rebuttal within a week, with a detailed list of objections, and an
>alternative classification. All the other subscribers reading this
>exchange can, if they desire, sign on as a reviewer at any point with
>questions or criticisms of their own for either taxonomist, and both
>A and B can respond directly to the questions and criticisms, even
>altering their classifications as they go along, in response (i.e.,
>real-time feedback). So, rather than a handful (or zero) reviewers,
>and one bout of editing, there can be dozens, even hundreds, and all
>without long delays or wasted paper. After a certain period, one or
>the other (or both, if neither has capitulated) would be "published"
>and officially available for use by the general public - meaning, in
>a practical sense, little more than a date stamp on a version the
>authors and reviewers agree is final; it might never need be
>committed to paper, if proper digital archive protocols are in place,
>and the whole thing might not even take a month from start to finish.
>So, instead of "Taxonomists who expect the world to await their final
>pronouncements", we would have taxonomists who have to appease
>anywhere up to hundreds of their critical peers, and possibly work it
>out in public with their detractors in an actual coutroom-style
>*debate*, evidence and all, and - even more - be able to edit,
>update, or completely retract their pronouncements, even after
>Under such a system, it seems unlikely that two (or more) opposing
>opinions could share the spotlight for long, and one could even have
>a vote solely for the purpose (and I stress the word "SOLELY"!) of
>deciding which classification should be adopted by the community as
>the one to be used in the Consensus Classification. No one is
>ultimately prevented from publishing their views (except, of course,
>if they cannot muster a single favorable review, which is the way it
>works with paper publication), and folks can keep track of
>alternative classifications in the master database, but at any given
>moment, there would be a single Consensus Classification available to
>that large pool of users who do NOT want to worry about
>contentiousness or flexibility. While I understand what Richard is
>getting at with his "I feel lucky" approach, I still do think that
>the user community will - on the whole - *resent* being told that an
>element of classification, be it order name, family, or species, is
>"ambiguous" or "tentative". If we want public support *for* taxonomy,
>I think we need to give the public something that won't leave them
>feeling queasy *about* taxonomy. For that matter, with the use of
>GUID's, changes in the Consensus can be instantly propagated
>throughout the entire dataverse, so no one ever has to rely on
>outdated information, nor ever wait for a consensus to emerge; the
>consensus opinion on a suggested change or addition would be made
>simultaneously with the act of publication.
>This is a RADICALLY different view of how the taxonomic community
>could operate than the context Meredith is thinking of, I'm certain -
>under the status quo, yes, consensus among taxonomists is definitely
>a pipedream, but the status quo assumes a fragmented community with
>no central meeting place, no one venue where everyone can interact.
>Now imagine how differently we could do things if we dump the status
>quo and choose instead to be a truly interactive community. This is
>*not* a fantasy, and I sincerely hope that you don't see it as such;
>it's a *choice*, available if we want it to be.
>Put it this way: if you were offered the chance to publish, quickly,
>for free, without page limits, without restrictions on graphics,
>tables, data matrices, or other ancillary materials, and knew that
>every other researcher in your field would be able to review your
>work (without fear of plagiarism, or unfair criticism), and that
>every reader who needed your work would have instant access to it,
>would you *refuse* to publish this way? If so, why? If none of you
>can say that you would refuse, then what exactly is keeping us from
>implementing such a system?
>That's essentially the "brass ring" that Richard says I'm suggesting
>we aim for. I don't see what we'd *lose* by attempting it, nor see it
>as a fantasy.
>Doug Yanega        Dept. of Entomology         Entomology Research Museum
>Univ. of California - Riverside, Riverside, CA 92521
>phone: (909) 787-4315 (standard disclaimer: opinions are mine, not UCR's)
>   "There are some enterprises in which a careful disorderliness
>         is the true method" - Herman Melville, Moby Dick, Chap. 82

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