[Taxacom] taxonomic names databases

Nico Franz nico.franz at asu.edu
Fri Sep 2 09:48:35 CDT 2016

I was going to take a break (this can't well be about 'winning'), but
perhaps one more item.

I find Sabina Leonelli's view fairly convincing that a deflationary view of
the status of our aggregation syntheses is not very appropriate. We hear
this view being expressed so often in the context of biodiversity data

Leonelli, S. 2013. Classification theory in biology. Biological Theory 7:
338-345. doi:10.1007/s13752-012-0049-z

   She writes in conclusion (page 344):

   I believe that there are important reasons for pointing to
classificatory activities as *theory-making* rather than simply as part of
the background knowledge or modeling strategies used in theorizing.
Probably the most important one is the role that such theory plays in
delimiting the content and development of knowledge (what counts as
biological insight, which form it can take); and as a target for critique
and reference points for the construction of alternative accounts. Some
classificatory systems systematically and synthetically express, rather
than simply affect, knowledge obtained through scientific research, and
they do it in a way that (1) is unique, since such knowledge is not
formalized anywhere else in the same way; (2) has huge influence on
knowledge-making practices; and (3) enables experimenters to make sense of
the results they obtain. At the same time, the conceptual framework these
theories provide only makes sense in light of specific traditions in
handling data. The role played by what I call classificatory theories
parallels Krakauer et al.’s (2011, p. 272) discussion of what they call
“bottom-theory” emerging from data handling practices: “Theory provides the
basis for the general synthesis of models, and a means of supporting model
comparisons and ideally establishing model equivalence.” Of course,
classificatory theories are best understood in relation to the collection
of models, instruments, and commitments made by the researchers who
produced it, as in the case of any scientific theory. However, they cannot
be reduced to any of those other elements; and they provide a way to link
and *evaluate* the epistemic results of using all those methods and tools
to research nature. Articulating knowledge that enables scientists to
assess and value their results is an achievement that goes well beyond
listing a set of commonly used assumptions as a basis for further inquiry.
In the latter case, existing knowledge is applied to put a given set of
items into some order; in the former, existing knowledge is transformed and
developed so as to facilitate the conceptual analysis of data. This is why
the results of some classification systems should be viewed as theories
rather than mere background knowledge—even if, as I have shown, this notion
of theory differs from traditional depictions as a series of axioms or
principles with great explanatory power and universal scope.

   Of course not all will agree with this view. But I think it is a
plausible position *for a taxonomist* to adopt. And that may mean that,
regardless of how certain aggregators prefer to perceive their activities
as merely this or that, for a good section of the expert community there
*is* a perception of novel theory making, and of novel theory making under
a design paradigm that can work to the exclusion of that heterogenous
community. A deflationary stance is not an effective way to work against
that perception. Acknowledgement does not negate the great value of
syntheses to some; instead I think it ultimately helps bring contributors,
users, and quality/trust issues closer together.

Cheers, Nico

On Thu, Sep 1, 2016 at 11:35 PM, Paul Kirk <P.Kirk at kew.org> wrote:

> OK, let me say it again - peer review is a myth. In that statement I mean
> it's never always as perfect as we want or imagine it to be, because
> perfection is also a myth. If an author is interested in 'brownie points'
> with an eye on a possible salary increase at the end of the year they go
> for a high impact factor journal to publish their manuscript, if not they
> set their sights lower, and there are journals out there falling over
> themselves for manuscripts to publish (never mind the quality, feel the
> width). And some journals ask the author for appropriate reviewers when a
> manuscript is submitted - isn't that the taxonomic equivalent of insider
> trading? I doubt that the WoRMS editors change classification on a whim -
> we are drowning in published trees right now and if the aforementioned
> editor sees a tree with a twig bearing a sequence tagged with a name they
> know in a family it's not currently placed in why wouldn't they adopt that
> new classification?
> 'What we want are experts at tracking and making sense of primary
> taxonomic literature' ... one persons 'sence' is another persons
> 'nonsense'. And tracking all the recent primary literature is impossible
> for most people because a proportion of it is behind a pay-wall.
> OK, off my soapbox now and back to editing Index Fungorum :-)

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