Richard Pyle - Implementing the Digital Taxonomic Revolution: Strategies for a Successful Web-Based...

Implementing the Digital Taxonomic Revolution:Alternate Strategies for a Web-Based Registry

of Taxonomic Names

Implementing the Digital Taxonomic Revolution:Alternate Strategies for a Web-Based Registry

of Taxonomic Names

Richard PyleBishop Museum

Honolulu

Richard PyleBishop Museum

Honolulu

Registration and PublicationRegistration and Publication

RegistrationThe process of entering a complete record in the ZooBank registry.

RegistrationThe process of entering a complete record in the ZooBank registry.

PublicationICZN-compliant published works, as defined in Chapter 3 (Arts. 7-9) of the 4th Edition of the ICZN Code.

PublicationICZN-compliant published works, as defined in Chapter 3 (Arts. 7-9) of the 4th Edition of the ICZN Code.

Available Name (Availability)A scientific name applied to an animal taxon that conforms to the provisions of the ICZN Code of nomenclature.

Available Name (Availability)A scientific name applied to an animal taxon that conforms to the provisions of the ICZN Code of nomenclature.

Registration and PublicationRegistration and Publication

The “Three Scenarios”The “Three Scenarios”Scenario #1

(Publication + Registration) = AvailabilityScenario #1

(Publication + Registration) = Availability

Scenario #2Registration = Availability

Scenario #2Registration = Availability

Scenario #3Registration = Publication = Availability

Scenario #3Registration = Publication = Availability

- ZooBank Technical Article, pp. 3-5- ZooBank Technical Article, pp. 3-5

- ZooBank Technical Article, pp. 5-9- ZooBank Technical Article, pp. 5-9

- Doug Yanega Post to ZooBank List, 22 Sep 2005- Doug Yanega Post to ZooBank List, 22 Sep 2005

Scenario #1:(Publication + Registration) = Availability


SummarySummary• To be available, names & acts must both

be published in accordance with existing Code rules, and be registered

• Registration can take place either before publication, or after publication

• If before or within 2 years after, date of availability is publication date; if more than 2 years after, date of availability is registration date*

• To be available, names & acts must both be published in accordance with existing Code rules, and be registered

• Registration can take place either before publication, or after publication

• If before or within 2 years after, date of availability is publication date; if more than 2 years after, date of availability is registration date*

Procedure (Pre-Publication)Procedure (Pre-Publication)

Journal/BookJournal/Book Taxon Author(s)Taxon Author(s) ICZN/ZooBankICZN/ZooBank

Submits online / hard copy form to ICZN with details of

nomenclatural act

Submits online / hard copy form to ICZN with details of

nomenclatural actAssigns GUID & returns form &

GUID to Author(s) with statement of Code compliance

Assigns GUID & returns form & GUID to Author(s) with statement

of Code compliance

Submits manuscript for publication, with GUID and copy of ICZN returned form

Submits manuscript for publication, with GUID and copy of ICZN returned form

Publishes name/act with GUID in full accordance with ICZN

Chapter 3 (Arts. 7-9)

Publishes name/act with GUID in full accordance with ICZN

Chapter 3 (Arts. 7-9)Sends copy of (relevant portion

of) published name/act & reference to ICZN, with original

form and GUID

Sends copy of (relevant portion of) published name/act &

reference to ICZN, with original form and GUID Verifies publication, makes GUID

public with registration detailsVerifies publication, makes GUID

public with registration details

Name is Available, using date ofPublication for priority purposesName is Available, using date ofPublication for priority purposes



Procedure (Post-Publication, within 2 years)Procedure (Post-Publication, within 2 years)

Journal/BookJournal/Book Author(s)/3rd PartyAuthor(s)/3rd Party ICZN/ZooBankICZN/ZooBank

Verifies publication and form for Code compliance, assigns GUID

& makes GUID public with registration details



Submits manuscript containing name/act for publication

(as normal current practice)



Publishes name/act in full accordance with ICZN Chapter

3 (Arts. 7-9)


3 (Arts. 7-9)Submits online / hard copy form

to ICZN with copy of (relevant portion of) published name/act & reference within 2 years of

publication date

Submits online / hard copy form to ICZN with copy of (relevant portion of) published name/act & reference within 2 years of

publication date

Name is Available, using date ofPublication for priority purposesName is Available, using date ofPublication for priority purposes



Procedure (More than 2 years Post-Publication)Procedure (More than 2 years Post-Publication)

Journal/BookJournal/Book Author(s)/3rd PartyAuthor(s)/3rd Party ICZN/ZooBankICZN/ZooBank










3 (Arts. 7-9)


3 (Arts. 7-9)Submits online / hard copy form

to ICZN with copy of (relevant portion of) published name/act & reference within 2 years of

publication date

Submits online / hard copy form to ICZN with copy of (relevant portion of) published name/act & reference within 2 years of

publication date

Name is Available, using date ofRegistration for priority purposes*Name is Available, using date of

Registration for priority purposes*



AdvantagesAdvantages

• Relatively small change to existing taxonomic practice

• Fast implementation via Amendment to the 4th Edition Code

• Maintains implicit quality control via traditional publication venues

• Perhaps broader acceptance by taxonomic community?

• Relatively small change to existing taxonomic practice

• Fast implementation via Amendment to the 4th Edition Code

• Maintains implicit quality control via traditional publication venues

• Perhaps broader acceptance by taxonomic community?



Disadvantages (and Rebuttal)Disadvantages (and Rebuttal)

• Somewhat complex procedure involving asynchronous publication and registration events, arbitrary time periods affecting date of availability, and petitions to the Commission in certain special circumstances

• Somewhat complex procedure involving asynchronous publication and registration events, arbitrary time periods affecting date of availability, and petitions to the Commission in certain special circumstances• Not really that complicated, in the context of all

the existing complexities of the ICZN Code• Not really that complicated, in the context of all

the existing complexities of the ICZN Code




• Somewhat ambiguous “gray zone” after publication and before registration when names & acts are “assumed” to be available, even though technically not available until registered

• Somewhat ambiguous “gray zone” after publication and before registration when names & acts are “assumed” to be available, even though technically not available until registered

• Most authors will probably register new names prior to publication, eliminating this problem entirely

• Most authors will probably register new names prior to publication, eliminating this problem entirely




• Still suffers from all the complexities and ambiguities associated with traditional paper-publication entangled with nomenclatural availability

• Still suffers from all the complexities and ambiguities associated with traditional paper-publication entangled with nomenclatural availability

• Not really much different from how it’s currently done, so not an increase in complexity

• Not really much different from how it’s currently done, so not an increase in complexity




• Requires (possibly extensive) increase in active role of ICZN staff (and associated costs) to process registration requests and verify Code compliance for issuance of GUIDs and exposing registration details to public

• Requires (possibly extensive) increase in active role of ICZN staff (and associated costs) to process registration requests and verify Code compliance for issuance of GUIDs and exposing registration details to public

• No rebuttal• No rebuttal



SummarySummary• The process of registration itself is all

that is required for availability of new names & acts

• Prior or subsequent publication through traditional venues is encouraged, but is not integral to nomenclatural availability

• The process of registration itself is all that is required for availability of new names & acts

• Prior or subsequent publication through traditional venues is encouraged, but is not integral to nomenclatural availability

Scenario #2:Registration = Availability



Journal/BookJournal/Book Taxon Author(s)Taxon Author(s) ICZN/ZooBankICZN/ZooBank

Registers name/act with ZooBank registry service, or submits hard-copy form with relevant minimum details to

ICZN for registration

Registers name/act with ZooBank registry service, or submits hard-copy form with relevant minimum details to

ICZN for registrationOnce Registration entry is complete, assigns GUID

automatically

Once Registration entry is complete, assigns GUID

automatically

Submits manuscript for publication, with scientific

rationale and full-blown description/details

Submits manuscript for publication, with scientific

rationale and full-blown description/detailsPublishes manuscript if

passes peer-review process (or not), with no implications for nomenclatural availability

Publishes manuscript if passes peer-review process (or not), with no implications for nomenclatural availability

Optionally sends copy/facsimile of publication & reference to

ICZN, linked to relevant Registration entry

Optionally sends copy/facsimile of publication & reference to

ICZN, linked to relevant Registration entry

Name is Available, using date ofRegistration for priority purposesName is Available, using date of

Registration for priority purposes




• Legalities of nomenclatural availability and science of taxonomy are disentangled from each other

• No ambiguity about date of Availability

• Existing complexities of nomenclatural availability of published works are moot

• Only minor increase to active role of ICZN staff (and associated costs)

• Legalities of nomenclatural availability and science of taxonomy are disentangled from each other

• No ambiguity about date of Availability

• Existing complexities of nomenclatural availability of published works are moot

• Only minor increase to active role of ICZN staff (and associated costs)




• Fundamental change to the way taxonomic names and acts are established (eliminating Publication process from act of nomenclatural availability)

• Fundamental change to the way taxonomic names and acts are established (eliminating Publication process from act of nomenclatural availability)• Not from the perspective of the taxonomists

(virtually same as Scenario #1)• Only change to technical legality of

nomenclatural availability, not necessarily change to taxonomic practice

• Not from the perspective of the taxonomists (virtually same as Scenario #1)

• Only change to technical legality of nomenclatural availability, not necessarily change to taxonomic practice




• More extensive changes likely needed in the Code, such that it could probably only be implemented in the 5th Edition of the ICZN Code (perhaps 5-10 years away; well past 2008)


• So be it – it will probably take several years to work out the details and demonstrate the feasibility via a working voluntary registration system anyway





• Taxonomists would lose their primary benchmark for establishing professional status (i.e., their CV’s would have fewer publications listed)

• Taxonomists would lose their primary benchmark for establishing professional status (i.e., their CV’s would have fewer publications listed)

• Professional status is established by publishing articles on scientific taxonomy and classification, which would continue exactly as before (only the legalities of nomenclature would be dissociated from publications – not the science of taxonomy)

• Professional status is established by publishing articles on scientific taxonomy and classification, which would continue exactly as before (only the legalities of nomenclature would be dissociated from publications – not the science of taxonomy)




• Journals might no longer publish taxonomic descriptions if the articles no longer carry the “prestige” of establishing new names and acts in accordance with ICZN rules

• Journals might no longer publish taxonomic descriptions if the articles no longer carry the “prestige” of establishing new names and acts in accordance with ICZN rules• Prestige in scientific publications comes from the

quality of the science content of the published articles; not from fulfilling a legalistic technicality for nomenclatural availability

• Prestige in scientific publications comes from the quality of the science content of the published articles; not from fulfilling a legalistic technicality for nomenclatural availability




• Elimination of quality control/peer review from process of establishing new names and nomenclatural acts

• Elimination of quality control/peer review from process of establishing new names and nomenclatural acts• No different from current situation or Scenario #1,

because the ICZN Code does not require peer review or quality control (nor should it?)

• No different from current situation or Scenario #1, because the ICZN Code does not require peer review or quality control (nor should it?)

• True, but the ICZN requirement for publication de-facto forces most names & acts through peer review

• True, but the ICZN requirement for publication de-facto forces most names & acts through peer review• No rebuttal• No rebuttal




• Bad taxonomists (and non-taxonomists) might abuse the system by registering hundreds of bogus and unneeded names, perhaps for unscrupulous reasons (e.g., selling names for money)

• Bad taxonomists (and non-taxonomists) might abuse the system by registering hundreds of bogus and unneeded names, perhaps for unscrupulous reasons (e.g., selling names for money)

• Again: no difference from current situation or Scenario #1, because the ICZN Code does not require peer review or quality control (e.g., self-publishing)

• Again: no difference from current situation or Scenario #1, because the ICZN Code does not require peer review or quality control (e.g., self-publishing)




• Lazy taxonomists might never get around to publishing the full description after the name is registered, potentially creating many names without robust taxonomic definitions

• Lazy taxonomists might never get around to publishing the full description after the name is registered, potentially creating many names without robust taxonomic definitions• Once again: no difference from current situation or

Scenario #1, because nothing is currently stopping lazy taxonomists from self-publishing minimalist descriptions that meet minimal Code requirements, exactly as a Registration entry would

• Once again: no difference from current situation or Scenario #1, because nothing is currently stopping lazy taxonomists from self-publishing minimalist descriptions that meet minimal Code requirements, exactly as a Registration entry would



SummarySummary• The Registration Web site hosts a full-

blown, edited, peer-reviewed online journal (like ZooTaxa) in which ALL names and acts must be published

• The science of taxonomy becomes part of the nomenclatural process (by Code)

• Submitted manuscripts are open to non-anonymous review by any interested or concerned taxonomist

• The Registration Web site hosts a full-blown, edited, peer-reviewed online journal (like ZooTaxa) in which ALL names and acts must be published

• The science of taxonomy becomes part of the nomenclatural process (by Code)

• Submitted manuscripts are open to non-anonymous review by any interested or concerned taxonomist

Scenario #3:Registration = Publication = Availability



Taxon Author(s)Taxon Author(s) ICZN/ZooBank/PublicationICZN/ZooBank/Publication

If ultimately accepted via the review process, names/acts are deemed to be formally registered

If ultimately accepted via the review process, names/acts are deemed to be formally registered

Manuscript is posted publicly, and open to non-anonymous review by any interested taxonomist

(automated alert system notifies community of new names/acts within their taxonomic groups of interest)

Manuscript is posted publicly, and open to non-anonymous review by any interested taxonomist

(automated alert system notifies community of new names/acts within their taxonomic groups of interest)

Submits manuscript for publication, with scientific rationale and full-blown

description/details, to single online journal administered by ZooBank

Submits manuscript for publication, with scientific rationale and full-blown

description/details, to single online journal administered by ZooBank

Revises manuscript, in accordance with comments & criticisms received from

online reviewers

Revises manuscript, in accordance with comments & criticisms received from

online reviewers

Name is Available, using date ofAcceptance for priority purposesName is Available, using date ofAcceptance for priority purposes




• All taxonomic publications would appear in a single venue (as is now done for Bacteria), instead of scattered across thousands of journals

• No longer the potential for one author to “steal” another’s work by trying to submit a plagiarized work to a journal that has a faster turnaround time

• All taxonomic publications would appear in a single venue (as is now done for Bacteria), instead of scattered across thousands of journals

• No longer the potential for one author to “steal” another’s work by trying to submit a plagiarized work to a journal that has a faster turnaround time




• All manuscripts are examined by a large contingent of reviewers, instead of just a handful, greatly improving the reviews as well as democratizing the process

• The reviews are public, instead of anonymous, so personal grudges or biases of the reviewers are exposed to scrutiny by the whole community

• All manuscripts are examined by a large contingent of reviewers, instead of just a handful, greatly improving the reviews as well as democratizing the process

• The reviews are public, instead of anonymous, so personal grudges or biases of the reviewers are exposed to scrutiny by the whole community




• A dedicated nomenclatural journal means that the review criteria will explicitly address all necessary aspects of code-compliance and proper nomenclature

• All the other advantages of an online review process (fast, iterative, open to bidirectional feedback, etc.)

• NO COPYRIGHT ISSUES!!!

• A dedicated nomenclatural journal means that the review criteria will explicitly address all necessary aspects of code-compliance and proper nomenclature

• All the other advantages of an online review process (fast, iterative, open to bidirectional feedback, etc.)

• NO COPYRIGHT ISSUES!!!




• Represents a MAJOR and fundamental change to the way taxonomy is done, both in terms of legalities of nomenclature and for the science of taxonomy

• Represents a MAJOR and fundamental change to the way taxonomy is done, both in terms of legalities of nomenclature and for the science of taxonomy

• With such major changes come major advantages, and the trade-off is worth it

• With such major changes come major advantages, and the trade-off is worth it




• Many taxonomic groups do not have many (or even any) experts who would serve as reviewers, and thus submitted manuscripts may never receive peer-review

• Many taxonomic groups do not have many (or even any) experts who would serve as reviewers, and thus submitted manuscripts may never receive peer-review• This problem is equally true for traditional

publication venues as well; but with only one “official” taxonomic journal with potentially thousands of regular participants, there is a better chance of finding someone who is qualified to review the manuscript

• This problem is equally true for traditional publication venues as well; but with only one “official” taxonomic journal with potentially thousands of regular participants, there is a better chance of finding someone who is qualified to review the manuscript




• Such a system would impose a huge burden on the taxonomic community to provide peer reviews to 20,000+ new names each year

• Such a system would impose a huge burden on the taxonomic community to provide peer reviews to 20,000+ new names each year

• No more burden than already exists: for every manuscript that is submitted and reviewed through the official ZooBank online journal, one fewer manuscript is submitted to a traditional journal (i.e., no net increase in total number of manuscripts to review)

• No more burden than already exists: for every manuscript that is submitted and reviewed through the official ZooBank online journal, one fewer manuscript is submitted to a traditional journal (i.e., no net increase in total number of manuscripts to review)




• Existing journals that depend on taxonomic descriptions and nomenclatural acts to fill their pages and maintain a subscriber base may be driven out of business

• Existing journals that depend on taxonomic descriptions and nomenclatural acts to fill their pages and maintain a subscriber base may be driven out of business

• Since when is it the job of scientists to keep journal publishers in business? Journals exist to serve scientists, not the other way around

• Since when is it the job of scientists to keep journal publishers in business? Journals exist to serve scientists, not the other way around




• The criteria for determining when a submitted manuscript should be deemed “accepted”, and when (and by whom) will always be a subjective and contentious issue

• The criteria for determining when a submitted manuscript should be deemed “accepted”, and when (and by whom) will always be a subjective and contentious issue• Each manuscript would be assigned to an

impartial “referee” (whose specialty is outside the particular taxon involved), who is fully versed in the ICZN Code – serving the same role as a journal editor

• Each manuscript would be assigned to an impartial “referee” (whose specialty is outside the particular taxon involved), who is fully versed in the ICZN Code – serving the same role as a journal editor




• The legalities of nomenclatural availability and the subjective science of taxonomy would, for the first time, be formally coupled under Code rules

• The legalities of nomenclatural availability and the subjective science of taxonomy would, for the first time, be formally coupled under Code rules

• And this is bad because....? • And this is bad because....?



(i.e., some people feel that quality control/peer review should be part of the Code requirements for nomenclatural availability)

(i.e., some people feel that quality control/peer review should be part of the Code requirements for nomenclatural availability)

References CitedReferences Cited

http://list.afriherp.org/pipermail/zoobank-list/2005-September/000003.html

http://list.afriherp.org/pipermail/zoobank-list/2005-September/000003.html

ZooBank Technical Article:ZooBank Technical Article:

Doug Yanega Post to ZooBank List, 22 Sep 2005:Doug Yanega Post to ZooBank List, 22 Sep 2005:

http://www.iczn.org/new%20ZooBank.htmhttp://www.iczn.org/new%20ZooBank.htm

Polaszek et al., 2005. ZooBank: the open-access register for zoological taxonomy: Technical Discussion Paper. ICZN Website. 10 pp.

Polaszek et al., 2005. ZooBank: the open-access register for zoological taxonomy: Technical Discussion Paper. ICZN Website. 10 pp.

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