[Taxacom] eol in nature

Richard Pyle deepreef at bishopmuseum.org
Thu Sep 6 20:47:15 CDT 2007

Thanks, Donat,

I'd like to amplify and comment on something from Vince's blogpost:

"The Encyclopedia should present a consensus that is an algorithmically
reconciled function of the discrepancies present in the underlying content.
For it to be useful the Encyclopedia must present ONE view to a naive user –
the algorithmic equivalent of Google News for biodiversity data. This
obviously won’t be the definitively correct view. In many cases it may not
even be the “best” view – but most importantly it will be ONE view of life
on Earth."

I have, for a long time now (back since the All-Species days, at least),
been championing a Google-News-like interface for EoL, and particularly the
use of algorithmically generated PageRank-like mechanisms for prioritising
the visibility of information in various categories on any given EoL Species

What I'm not sure I understand, however, is how this equates to "ONE view".
One of the things I like about the Google News interface is that it gives me
access to multiple perspectives on stories, all in one place.  Through a
little bit of meta-analysis, it's pretty easy to find the undisputed facts
as consensus opinions emerging from the noise.  In such an environment,
ID/creationist persepectives wouldn't stand a chance -- even to the naïve

Even in terms or presentation, Google News allows me to customise what
categories of stories I'm most interested, where they appear on the page,
and how many headlines per category.  I would like to see the same sort of
customization on EoL, where any user can flavor it to their preferences
(taxonomists, vs. ecologist, vs. bird watchers -- and maybe even
Creationists -- though I don't know how, exactly they would set paramaters
to allow them to see only what they want to see...)

Maybe I misunderstand Vince's concept of "one view".  And, other than this,
I am complete agreement on the idea of Google-like algorithmic approach to
prioritizing data (except in the case of EoL, the algorithm should be
completely open and visible to all).

I also diagree with Donat that the expectations are for new content, rather
than "regurgitated" data.  In my understanding, EoL is intended as an
organizer of exisiting information (again, much like Google), rather than a
generator of new content.  In the best of all worlds, EoL will do for
biodiversity data what HotBot/Google/Yahoo/etc. (with a component of
Wikipedia thrown in) did for the web: that is, make access to biodiversity
information much easier.

I'll tell you why I, as a taxonomist, would want to contribute:  because the
very existence of an EoL (under any moniker, or resulting from whatever
grand initiative) gives me something in return.  In fact, it gives me two
things.  First, it makes my own contributions much more visible to the rest
of the world; and second, it gives me much easier access to information I'm
interested in.

Taking your example of linking a Protonym to a subsequent name usage, I'm
getting tired of having to make this association multiple times (once for
Bishop Museum's database, once for PBIN/NBII, once for ITIS, once for
Species 2000, once for the Catalog of Fishes, once for FishBase, once for
GBIF, once for ZooBank....etc., etc.)  I want an infrastructure that allows
me to do this ONCE PERIOD, and have every dataset of relevance know about it
automatically.  The tools and protocols that TDWG and GBIF and EoL (each
with their respective roles) are all aiming for, and getting closer to, will
allow for the creation of such an infrastructure. One of the mantras of the
All-Species Foundation was "Once digitized, always available".  The point
being, we have been wasting LOTS of time repeating the same effort over and
over again, simply because our digitization efforts have not been adequately

I know I always seem to be the cheerleader for these "grand initiatives",
and maybe my professional reputation suffers for it.  But damn it, we all
KNOW it's possible, and the vision is right.  One of these days it will
actually happen.  And until that day comes, I've got my pom-poms at the


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Donat Agosti
> Sent: Thursday, September 06, 2007 3:15 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] eol in nature
> One of the strength of EOL is the art of orchestrated PR, one 
> bit in NYT another at the same time in Nature
> http://www.nature.com/nature/journal/v449/n7158/full/449023a.html
>  (for those having access to Nature)
> And here is a first comment I just got http://vsmith.info/EOLinNature
> I would probably agree, that the expectations are now raised 
> for delivery of new content (not regurgitation of what is 
> there somewhere else already), that making it right for 
> everybody and thus stepping beyond the scientific world 
> without confusing our 'scientific' message will be a tricky task.
> The question is not answered yet, why a taxonomist wants to 
> contribute to this if he doesn't get anything out in return. 
> For example, names are in publications and might be able to 
> recovered. But who can reconcile all these names, that is, 
> produce the link between the protonym and the new variant?
> If the machine ought to do this, then there are a lot of 
> errors and specialists pages will remains the resort for the 
> information eol wants to provide.
> Donat
> NATURE|Vol 449|6 September 2007
> Taxonomy: The Collector
> Top of page
> Abstract
> How Paddy Patterson, one of the architects of the 
> Encyclopedia of Life, hopes to present biodiversity to the world.
> David 'Paddy' Patterson started his career off small, working 
> on the taxonomy of protists and protozoa and putting 
> descriptions of them up on the web in projects such as 
> Micro*scope, Microbial Life and the International Census of 
> Marine Microbes. Now, the biologist, who works in Woods Hole, 
> Massachusetts, is going macro in a big way with the 
> Encyclopedia of Life (EOL), a project that intends to create 
> a website for every known species on Earth.
> So what is the proposed schedule for the EOL?
> In February next year, hopefully, there will be a major 
> release of the first edition of the EOL. The expectation is 
> that within a ten-year period we will have relatively 
> well-informed pages on all 1.8 million species.
> How can you realistically hope to get that much done?
> The EOL will act like a glue to join together the information 
> that is already out there on the Internet. We don't have to 
> create 1.8 million pages. What we need to do is know where 
> the information is that's out there on the species.
> How do you put it together?
> The usual solution is to try and find out what the correct 
> name is for a species and then try to get all the databases 
> to apply the correct name. But names are always changing as a 
> result of taxonomic research.
> We adopted a different solution, which we call 
> reconciliation. What we do is tap into the accumulated 
> knowledge of taxonomists and draw together their 
> understanding of all the different names that have ever been 
> used for an organism, and extend this to cover typographical 
> errors, vernacular names, and any name that might appear in a 
> document that is online or a database that is online.
> We've built the system so that you can have any browsing 
> structure in place.
> So if you want to change from the hierarchy provided by the 
> Catalogue of Life [an attempt to index all known species] to 
> that provided by GenBank [a database of all published DNA 
> sequences], you just click on the alternative classification.
> How far should that flexibility extend? You previously 
> mentioned making room for an intelligent-design perspective 
> on the EOL?
> Many bits of the EOL still need to be resolved, but one of 
> the features of the EOL is that it has to be a highly 
> flexible, very personalizable environment. If the EOL is to 
> fulfil the role that we think it should fulfil, then students 
> at high school should see something different from, for 
> example, what a research scientist sees. Similarly, people 
> visiting from Pakistan should be able to see the content in a 
> language that suits them and is not culturally offensive to them.
> And the same thing is true, I think, of people who hold 
> beliefs such as intelligent design or the creationist 
> argument. It would be, in my view, a great failing if we 
> created an environment that they found offensive and were 
> unwilling to enter. They are, after all, probably the 
> community we would most like to see develop a better 
> understanding of biodiversity and how biodiversity came about.
> That sounds like a controversial approach?
> It was. Plenty of people would have me hung up by my 
> whatever-it-was for this.
>     Plenty of people would have me hung up by my 
> whatever-it-was for this.
> My view is that by giving the stage to this community, what 
> they're thinking becomes open to wider scrutiny. Instead of 
> talking in closed churches, now the public can see the extent 
> of their thinking. I see it as something that should improve 
> the knowledge environment in general.
> You're obviously very keen on involving people in the project 
> as widely as possible?
> Some of the features we're developing will be rather like 
> wikis or the social networking software out there. One of the 
> things I would love to see develop early on is a 'my 
> schoolyard' function in which kids can go outside with cell 
> phones and take pictures of organisms and submit them to the EOL.
> There, the pictures are sent off to experts who verify 
> identification. And when that is done, a little dot appears 
> on Google Earth showing the presence of, say, a daffodil in 
> someone's backyard.
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