FW: uBio & Free taxonomic information

[Richard Pyle]

> A point which, if your version is accurate, was not (at least not to
> me) made clearly until now.

Fair enough....and as I said, my comments were based on my own personal
perception of what uBio is trying to do.  Based on the off-list note I
received from Dave Remsen, I gather that my perception is pretty close to
the mark.

> But if it doesn't make that distinction, then it simply helps a
> larger audience of non-taxonomist users make mistakes confounding one
> for the other.

Yes, there is that cost.  But I would argue that it doesn't "simply" do
that.  You emphasize the cost/risk, but you also need to acknowledge the
benefit.

Here's the way I envision it (slipping into metaphor mode):

A Dictionary consists of both a list of words, and a definition of the
meaning (circumscription) of the words.  A Thesaurus is a cross-referencing
of different words that have related, similar, or identical meanings.  An
Index is a simple list of words, with links (via page number citations) to
information of relevance to those words within the body of a publication.

So...think of the "words" as taxon names, the Dictionary definitions as
taxon concepts (circumscriptions, or the defined *meaning* of the words),
the Thesaurus as the complete cross-referencing of historical synonymies,
and the Index....well, there really isn't much of an analogy to this on a
large scale within the field of Taxonomy (uBio is trying to create it).

My understanding of what uBio hopes to do is:

1. Generate a list of unique names (words), without necessarily attempting
to generate the circumscriptions (dictionary definitions) of those names.

2. Build an Index of occurrences of those names within published literature,
with direct links to associated information contained within the
publications.  Unlike more traditional Indexes at the back of a single book,
this Index is intended to (eventually) span all published works since the
time of Linnaeus (thanks to the Library Community's ongoing efforts to
digitize publications).

3. Build a Thesaurus of names (as derived from a subset of information
Indexed in step 2 above -- published historical synonymies), so that names
with some relevance to each other are cross-referenced.

What we have now in Taxonomy is a Dictionary that is woefully incomplete,
with patchy and disorganized associations between words and their
corresponding definitions.  Our Thesaurus is likewise scattered and
depauperate, and not cohesive.  And as I said before, the Index barely
exists at all.  What we do have is a growing list of "words" (via ITIS,
Species2000, IPNI, Catalog of Fishes, etc.), and some efforts to fill in
definitions.

If uBio is successful, then we will have a lot more to work with than we do
now -- at the very least a more complete Thesaurus and a robust Index.
Whatever time we taxonomists generally spend retrieving historical Thesaurus
entries and manually searching for published information without the aid of
a comprehensive index, we can now use to focus on what I think is the best
use of our time:  elucidating the definitions of the words as we begin to
flesh out the complete dictionary.

In other words, I see uBio as developing an infrastructure upon which we can
globally organize our taxonomic assertions about circumscriptions -- not
altogether unlike your envisioned "Manifesto", Doug....

> Sure, it's a nice thing to be able to look up every
> reference to "Aus bus" through history, but if someone revised Aus in
> 1990 so there are now 3 species where there used to be one, then
> unless you're flagging all references to "Aus bus" with a warning
> that all records before 1990 are potentially erroneous, there's going
> to be a lot of people working with an outdated concept and not realizing
it.

That is EXACTLY the point of the Thesaurus.  Suppose that Aus bus was
described in 1950, and in 1990 was split into A. bus, A. cus, and A. dus.  A
search on "Aus bus" in the uBio Thesaurus would generate an Index to both
pre-1990 *and* post-1990 citations of Aus bus.  If the user interface is
designed well, then it will be obvious to the user that citations to Aus bus
pre-1990 should be understood to be potentially inclusive of what are now
regarded as bus+cus+dus.  In other words, the warning would be not only
self-evident, but downright informative (with direct links to the
publication content, so that pre-1990 citations to the name could be
interpreted in the context of the post-1990 split).  This is all objectively
obtainable information, without the need for sophisticated taxonomic
insight -- the 1990 publication splitting one species into 3 is very
straightforward information.  Like I said, it's all in how the information
is formatted and presented in the output. But before we get to that stage,
the information needs to be organized electronically.

> You're
> assuming that these warnings and red flags would be built into the
> system, I'm assuming that they can only be built into the system if
> the system is built by taxonomists.

In a sense it *IS* built by taxonomists -- via their published assertions
about valid and synonymous taxon names. It doesn't take a seasoned
taxonomist to read and understand the 1990 paper that split Aus bus into 3
species.  Remember, the Index says NOTHING about whether the split was
justified, or "correct" -- it just objectively records the fact that the
1990 publication treated Aus bus as sensu stricto, whereas pre-1990
publications treated it prior to the existence of cus & dus (and therefore
sensu lato). Note that I'm not assigning special meaning to the terms
"stricto" or "lato", and I doubt those actual terms would be used in the
lay-person's formatted output.  But the output WOULD (presumably) visually
represent the fact that in 1990, the previously existing Aus bus was split
into 3 species, and by inference acquired a new meaning (without necessarily
defining that meaning).

> It's the same problem with
> databasing old museum specimens: if no one has examined the specimens
> in 50 or 100 years, who's to know whether the names on the labels are
> correct according to modern opinion? Sure, I love the idea of museum
> databasing - I engage in the practice myself - but ONLY for material
> which has been examined recently by an expert taxonomist. I find it
> hard to be in favor of any information management approach that
> cannot distinguish the good from the bad.

We are polar opposites on this one!  The old/historical specimen
determinations are EXTREMELY valuable, because they are the best markers we
have to retroactively scoping the boundaries of historical circumscriptions.
If you're saying that an electronic listing of old/outdated specimen
determinations is worse than no electronic listing at all, then I
wholeheartedly disagree.  If your point is more about limited curator time
and setting priorities, then that is an altogether different issue.

> That seems like a tall order for anyone besides a revisionary
> taxonomist to accomplish: it takes a lot of research to know which
> name combinations have been used to represent a given taxon
> throughout its history.

No it doesn't -- all it takes is the ability to automatically index what
names *have* been used in the literature, and the small amount of
generalized taxonomic understanding to recognize when an published reference
lists a species as valid, or as a junior synonym of another name.
Rudimentary stuff. The circumscription assertion itself is the part that
does require significant taxonomic insight (i.e., the work that went into
deciding that one species should be regarded as a junior synonym of
another). But that's the role of the actual publication -- not the Indexing
service.

> This is obviously going to be problematic for most of the genera on
> my web page - genus names like Box, Car, Chaos, Cylinder, etc. are
> not exactly easy for a text-matching algorithm to recognize as being
> biological names, are they?

I don't know -- but as I said before, the automated index will NOT BE
PERFECT.  But I think it's a lot easier to argue that the overall benefits w
ill exceed the costs or limitations, than it is to argue the converse. Maybe
this is where I am the one who is missing the point.

> It hurts if it takes resources away from taxonomy. You claim that it
> doesn't, and I'm willing to give the benefit of the doubt, but I'm
> not so sure. The implication is that the entities funding this
> initiative would never give money if they knew it was being spent on
> taxonomy, and that seems a little hard to accept.

As I said before, I made that claim based on more than speculation.  There
is a LOT of money out there for the Library community, that is not
immediately available to the taxonomic community (been there, tried that).
That is NOT to say that such monies couldn't eventually be made available
more directly for taxonomic purposes -- but I think we've got a ways to go
yet before we achieve the level of intra-disciplinary cooperation needed to
persuade these kinds of money sources to look in our direction.  I can't
speak with absolute authority, but I am quite confident that the money used
to fund uBio came from a source that otherwise would not have been willing
to support taxonomic research, per se.

> Perhaps, if it leads to uncritical acceptance and promulgation of
> errors by layfolk that could have been avoided by consulting a
> taxonomist. Perhaps, if it further marginalizes taxonomists and their
> efforts.

Yes, perhaps -- but as I tried to outline above, I don't think there is any
sound reason to believe that the generation of such an Index will lead to
such error promulgation.  It's hard to argue that the act of organizing
information is more bad than good.  There are certainly risks as you've
outlined, but that has much more to do with how the information is
presented, than the mere act of building tools that will organize the
information.

> If it doesn't distinguish valid from invalid taxonomic concepts, as
> you admit, then it appears to automatically and unavoidably devalue
> the efforts of taxonomists.

I'm not sure I understand your point.  The Index does not, itself, make
assertions about what names are valid and what names are not valid.  But it
WOULD chronicle how taxonomists over the years have (through their published
works) treated various names.  It would SHOWCASE the efforts of taxonomists.

> I guess here's where it's my turn to be skeptical: are we really
> going to have every piece of scientific literature ever published in
> history (not just taxonomic - ALL of the literature in existence
> which might refer to biological names) scanned, digitized, and
> converted into searchable text within the next few years?

I don't know....given the accelerative nature of technology, it's hard to
say (there's a famous quote by Bill Gates questioning whether desktop
computers would ever need more than 1MB of RAM...).  I've also been told of
possible large-scale funding efforts not far in the future that might target
exactly this issue. (Watch this space...)

But remember, uBio is developing the TOOLS, not attempting to generate the
full-scope content.

> Lawyers are "parasites" by this definition as well, but they control
> the commodity they deal in, and get paid well for it.

Hmmm....not sure I'll touch that one (using the legal profession as a
metaphor for taxonomy...) But in my own naive way, I have higher
aspirations -- as I said -- to define the taxonomic field as something more
substantative.

> Who says my opinion, or Chris', or Una's, are popular?

I was referring to the relative abundance of "pro" vs. "con" posts in this
thread (the former pretty-much coming only from Dave Remsen, as far as I
saw).  But now that you mention it, the off-list response to my post has
been essentially the opposite (5 and 0), so maybe I misjudged which side of
the argument was the more popular.

Aloha,
Rich