[Taxacom] Economist leader addressed to taxonomists: open access

Donat Agosti agosti at amnh.org
Fri May 18 17:50:09 CDT 2007


Reading through the Economist articles, the cases mentioned refer explicitly
to cases in the context of science (the Preble's meadow jumping mouse, the
polar bear) and implicitely to other, such as the raise of many primate
subspecies to species level, all of which happened with great fanfar and
often in collaboration with sophisticated PR tools in hand (such as the
monkey case).

Since there is a lot at (conventional economical) stake, more conservative
forces look at the bases of that and of course figure out, how week the
argument often is. And if you go out to the press, the press will hit back,
a story many famous people had to learn. Unfortunately, these are the rare
high profile cases, and we might think twice in future how to handle them.

Besides the Linnaeus article, the one referred to though is right to the
point that there is still a lot to be discovered, and actually rather shows
the fascination of how little is known out there.

It's always good to write to editors - but then complaining doesn't help,
unless you have a solution. EOL might be an answer to this, though it will
first have to stay the test of time and move from an empty shell to a real
thing - a potential it has at this moment. But I would also urge all of you
to make our science more high profile by making all your publications open
access at least through self archiving. It would also support EOL who's
Biodiversity Heritage Library Component is only part of what we want, access
to systematics literature in full, since they do not touch most of the
modern literature, that is anything younger than 75 years old for which they
do not have an explicit go ahead from the publishers (nota bene: publisher
and not author).

What I suggest is the following.
1. Self Archive all your publications. Ask your institution to help, there
are all tools available to do so
(http://www.earlham.edu/~peters/fos/overview.htm). More than 92% of the
journal allow self archiving, either as pre- or postprint. If you have a
proper self archive, it will be picked up by search engines such as google.
2. Build up thematic literature archives (eg http://antbase.org)
3. Do not publish in journals that do not allow self archiving
4. Make your institution sign up the Berlin Declaration on Open Access, a
world wide movement.
5. Do not transfer the copyright of the publication to the publishers but
the right for publication and commercial usage. Science Commons just
launched a package to write up such an amendment to standard contracts
(http://sciencecommons.org/weblog/archives/2007/05/17/scae-launch/).

More sophisticated approaches are:
6. Ask the publisher to release an xml (eg as an example
http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F1
0.1371%2Fjournal.pone.0000423 in PLoS One) version of the papers including
some taxonomic specific mark up like taxonx. This allows ispecies, hopefully
EOL and others to pick up the descriptions of a particular species, or
datamining, and would not only provide open access to the literature, but
much more sophisticated searches then google will be doing, since the begin
of taxonomic description is known, and thus that everything in it belongs to
a particular taxon.
7. Lets look into dedicated journals which include such mark up and help to
describe all those millions of species in a much more efficient way as we
can do, feed directly into such initiatives like Zoobank and thus show the
increase of species we discover.
8. Add to all the specimen record a unique identifier, such as a doi, so
that in future arguments all the underlying data can be retrieved and
re-analysed to get at least this sore point in discussions out. Dito for
gene-sequences, morphological data, images..


Finally, let's make sure that our taxonomic data is really properly being
used in conservation, that is build a link from specimen data up to policy
decision, not interrupted by so called expert opinions who draw, based on
their insights draw circles which are then used to defining hotspots ore
global amphibian assessments. These are high profile, but fail the test of
reproducibility and thus are easily open for the kind of challenges
mentioned in the Linnaeus editorial - they also do not allow measuring the
loss of biodiversity properly, something which should be able to do for the
countdown2010, but I am afraid, we once again will fail.

The points above to not cost a lot, but have a tremendous impact, and only
through this, our data will be used more frequently, be if through EOL or
other search engines which might as well appear, if there is enough data out
there which can be easily mashed up, which is not really the case right now.

Donat 



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of David Patterson
Sent: Friday, May 18, 2007 2:44 PM
To: Roderic Page; TAXACOM
Subject: Re: [Taxacom] Economist leader addressed to taxonomists

Folks

I agree with Rod as to the tone of a response - and I do 
believe one should be written.  Would Rod be willing to 
write a first draft?

I would add two points.

The EOL is a major taxonomic initiative that has the 
capacity to accelerate consensus, and therefore 
consistency, stability, and discovery. This is the mature 
response to the concerns of the 'what is a species' issue.

The response to EOL has been stunning, we have received 
tens of thousands of positive enquiries, which gives us 
another argument - that some of the comments in the 
Economist grossly fail to represent prevailing opinions 
and so are disengenuous.

The manipulative aspects of some of the points in the 
Economist takes me back to Donat's mailing some time ago 
of the pit bull - which I suspect has now become a real 
issue.

David Patterson




On Fri, 18 May 2007 10:15:23 +0100
  Roderic Page <r.page at bio.gla.ac.uk> wrote:
> So, once again taxonomist's heckles are raised, and the 
>response is  
> "they don't understand how important we are!", "we don't 
>have enough  
> money!", etc.
> 
> Is this the best way to respond, especially to this 
>audience (leaving  
> aside the issue of whether the article was justified or 
>not)?
> 
> Why not think about responding in terms the audience 
>might  
> appreciate? I wonder, for example, whether there are 
>parallels  
> between biologists making bad decisions based on 
>misunderstanding  
> relationships between organisms, and business failing 
>because their  
> supposedly homogeneous target market of, say, 
>"teenagers", turned out  
> to be highly heterogeneous (niche marketing, anyone?).
> 
> One could even draw parallels with recent foreign policy 
>decisions,  
> based an appalling lack of understanding that "muslims" 
>are not a  
> homogeneous category.
> 
> Complaining about money is a bit of a hard sell, given 
>that EoL has  
> been launched to such fanfare. Yes, I know it's not 
>money for people  
> in the trenches, but to have major charities committing 
>money, flashy  
> videos, and $US 100,000 promotion campaign (albeit "in 
>kind"), and   
> don't you think Economist readers will wonder what 
>taxonomists are  
> complaining about...
> 
> Regards
> 
> Rod
> 
> 
> 
> On 18 May 2007, at 09:35, Maarten Christenhusz wrote:
> 
>>
>> Dear all,
>>
>> In reactoin to this article in the Economist, I think we 
>>would do  
>> well to write a counter article from a variety of 
>>taxonomic fields  
>> (both plants and animals, macro and micro organisms) to 
>>explain to  
>> the Economist how important taxonomy is, what the 
>>differences are  
>> from systematics and conservation biology, that taxonomy 
>>is the  
>> basis of all biological studies, and that we are heavily 
>> 
>> underfunded, probably because the discipline is heavily 
>> 
>> misunderstood by the wider public. I would be very 
>>willing to  
>> participate in this, but as a vascular plant scientist, 
>>my  
>> knowledge on primates and the microbial world is 
>>limited. Shall we  
>> write a counter article on taxonomy to the Economist? 
>>Who's with me?
>>
>> Maarten Christenhusz
>> Dept. of Biology, sect. Biodiversity
>> University of Turku
>> 20014 Turku
>> Finland
>> www.botanyphotos.net
>>
>> ----- Original Message -----
>> From: Barry Roth <barry_roth at yahoo.com>
>> Date: Friday, May 18, 2007 7:34 am
>> Subject: Re: [Taxacom] Economist leader addressed to 
>>taxonomists
>>
>>> Thank you for the cheering example of a much better 
>>>researched
>>> article -- including the revelation that Prof. Daniel 
>>>Brooks makes
>>> phenetic ("magnitude of difference") judgments regarding 
>>>the rank
>>> of taxa he deals with.
>>>
>>>  Barry Roth
>>>
>>> "Frederick W. Schueler" <bckcdb at istar.ca> wrote:
>>>
>>> * well, here's a less ignorant take from a mainstream 
>>>newspaper:
>>>
>>> Subject: Press: The Trouble With Taxonomy
>>> Date: Mon, 14 May 2007 10:27:11 -0400
>>> From:
>>> To:
>>>
>>>
>>> ---------------------------------
>>> Get your own web address.
>>> Have a HUGE year through Yahoo! Small Business.
>>> _______________________________________________
>>> Taxacom mailing list
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>>
>>
>> _______________________________________________
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>>
> 
> ----------------------------------------
> Professor Roderic D. M. Page
> Editor, Systematic Biology
> DEEB, IBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QP
> United Kingdom
> 
> Phone: +44 141 330 4778
>Fax: +44 141 330 2792
> email: r.page at bio.gla.ac.uk
> web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> iChat: aim://rodpage1962
> reprints: 
>http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
> 
> Subscribe to Systematic Biology through the Society of 
>Systematic
> Biologists Website: http://systematicbiology.org
> Search for taxon names: 
>http://darwin.zoology.gla.ac.uk/~rpage/portal/
>Find out what we know about a species: 
>http://ispecies.org
> Rod's rants on phyloinformatics: 
>http://iphylo.blogspot.com
> Rod's rants on ants: http://semant.blogspot.com
> 
> 
> 
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David J Patterson
Encyclopedia of Life
Marine Biological Laboratory
Woods Hole
Massachusetts 02543
USA

Phone: 1 508 289 7260
FAX: 508-457-4727

http://www.eol.org
http://eolinformatics.mbl.edu
http://microscope.mbl.edu
http://www.mbl.edu/research/resident/lab_baypaul.html

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