[Taxacom] human involvement (was Re: BioNames)

Scott Thomson scott.thomson321 at gmail.com
Wed Jun 5 07:58:51 CDT 2013


Hi everyone,

its been suggested that I should clarify my previous post. I apologise if
anyone was confused apart from being a zoologist I also did a Software
Engineering degree and got a little caught up in the jargon from that
degree. I said I did not think a software package should be freeware. Ok
Freeware is a licence, a term and basically means that the software is
entirely free, including development. A software package can be free of
charge to the end user but not be freeware. So what I am suggesting is that
a software package be developed for nomenclature but that it be developed
and maintained professionally, this will generally require them to be paid
or funded to do this, of course the developers can then distribute it at no
cost (free) to the users if they so desire, but this is not freeware. An
example of this would be Adobe PDF Reader, completely free to the end user
but the development team are paid, it is professionally developed.

I hope that clarifies that point for anyone unsure of what I meant.

Cheers, Scott


On Tue, Jun 4, 2013 at 10:58 PM, Roderic Page <r.page at bio.gla.ac.uk> wrote:

> Doug, Bullying may overstate things, but I've heard "let's make it
> mandatory" come up in several contexts (e.g. archiving phylogenetic trees)
> and it often seems accompanied by a lack thinking about how to create a
> situation where people would see doing something as a no brainer.
>
> Funding agencies mandating open access for they fund, for example,
> certainly focussed people's minds. But sites like http://figshare.commanage to make a compelling case for open sharing with any compulsion.
>
> The benefits you list are great, if a little abstract (in that there's not
> much that is immediate and tangible for the user). It's been a while since
> I've actively done taxonomy - can you tell ;) - but some things which
> strike me as basic needs are 1) have I got all the relevant papers on this
> group? 2) have I got a list of all the species? 3) where are the types? 4)
> who else is working on this group? The number of times people ask on
> TAXACOM for literature should tell us something.
>
> GenBank has reached the point where it's the first place many people go to
> so their research. Want to study the phylogeny of 'x'? Go to GenBank, grab
> sequences, build trees, decide where gaps are. It is not just the place you
> go to at the end of your study to archive your data.
>
> So, identify the points of pain for people doing taxonomic research,
> figure out if there's a way to tackle those that could also generate a
> resource that benefits the wider taxonomic community. If you have to
> mandate something then ultimately you're doing it wrong (tongue only partly
> in cheek).
>
> Regards
>
> Rod
>
> Sent from my iPhone
>
> On 4 Jun 2013, at 18:22, Doug Yanega <dyanega at ucr.edu> wrote:
>
> > On 6/4/13 12:49 AM, Roderic Page wrote:
> >>
> >> On 3 Jun 2013, at 23:13, Doug Yanega wrote:
> >>
> >>>
> >>> Realistically, one either needs to improve the incentive for
> >>> participation in the system (such as making participation effectively
> >>> mandatory, as happens with GenBank),
> >>
> >> Why must the incentive be making it mandatory? Ultimately this seems
> lazy  "you must do this because we can't think of a way to make it worth
> your while." It also requires that people can be bullied into compliance.
> > First, note that I said "such as" - for the reason you yourself point
> out; there are certainly other ways to accomplish this.
> >
> > Second, what is intrinsically wrong with mandatory? Does the scientific
> community truly feel that being told "everyone needs to submit their gene
> sequences to GenBank in order to publish" is a form of "bullying"? Part of
> the scientific method is giving others the data to see how you arrived at a
> given conclusion, and that's what access to sequence data affords, in
> addition to vital descriptive functionality. I gave the GenBank example
> because that is the exact same context I envision, except that instead of
> gene sequences, what is required is links/cites to fully-resolved ZooBank
> records for every scientific name one uses in a publication. For authors
> working on popular taxa, the odds are that any taxon name they intend to
> publish will already be recorded, and all they need is to look it up and
> link/cite it. For authors working on more obscure taxa, they will often
> need to personally enter the     information into ZooBank as part of their
> authorship responsibilities - just as authors need to register their gene
>   sequences in GenBank now. Given that no one should be doing taxonomy
> without access to the original literature, requiring that an author
> transcribe the pertinent data into ZooBank is not adding very much to their
> overall effort.
> >
> > Third, I'm sure that you, Rod, of all people, can imagine ways to not
> only link to the ZooBank record, but simultaneously link to the original
> description, such that every time someone uses a scientific name, the work
> in which that name was coined gets cited in a manner that counts towards
> academic citation metrics. This would give some added incentive for people
> doing alpha taxonomy, if any time someone publishes one of your taxon names
> you get cited in the process. Right now, it is essentially unheard-of for
> any biologist to cite the works in which his/her study organism(s) were
> described, which - arguably - makes alpha taxonomy seem less academic than
> other disciplines. Heck, maybe this could be extended to give credit to the
> person who identified one's study organism(s), as well. Both these measures
> would improve things for both the readers of biological works AND the
> taxonomists - whose efforts are presently going unrecognized outside of the
> "Acknowledgments" sections (if that).
> >
> > Fourth, having links/cites to ZooBank records would also allow for
> backwards propagation of new information. Consider what happens if
> someone in 1950 published on, say, the gray hairstreak butterfly
> Ministrymon azia in Texas. Given that just this month a new sympatric
> cryptic species has been split off, then that 1950 paper would not
> necessarily be about the species that the author in 1950 thought it was
> about, and people (other than butterfly specialists) who read that paper
> might never know that there was any question about the actual species
> identity. Now imagine if a present-day author published a paper like that
> but with a ZooBank link, and 10 years down the road, the species they
> studied is split. If that ZooBank record is (upon publication of the split)
> converted into a disambiguation link that shows the records for both the
> original taxon and the new taxon, then *anyone* who reads that outdated
> paper will know that the species was split without ever themselves having
> to do any literature searches to track down the changed status.
> >
> > Again, requiring the registration of names one is using is a small
> imposition on authors, with a very large potential for benefit (for both
> authors and readers), and it distributes the labor of populating the
> registry to those who are actively using the names (and motivated to do it
> correctly).
> >> What if we had a tool that offered enough value to individuals that
> they wanted to participate? That solved a         problem that users had,
> and as a by product built something of broader value? This, to me, is the
> lesson of Mendeley. You tackle the individual point of pain, and
> incidentally get people to build what you wanted them to build for you.
> Alternatively, you make an experience so compelling that you have to join
> ("wadda you mean you're not on Facebook?").
> > I agree that such an approach is desirable, and apologize if you
> gathered otherwise from my comments. Folks like Rich Pyle and myself are
> all ears if you have specific ideas along these lines!
> >
> > Sincerely,
> > --
> > Doug Yanega      Dept. of Entomology       Entomology Research Museum
> > Univ. of California, Riverside, CA 92521-0314     skype: dyanega
> > phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
> >              http://cache.ucr.edu/~heraty/yanega.html
> >   "There are some enterprises in which a careful disorderliness
> >         is the true method" - Herman Melville, Moby Dick, Chap. 82
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-- 
Scott Thomson
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