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The myth of coding from specimens firsthand and the untapped resource of photos



I posted this on my blog today, but think it's important enough to cross-post 
here.


You've probably heard it many times.  Advice from professional paleontologists 
about the proper way to code specimens.  For instance, here's Brochu from the 
DML in 2000-

"One thing I've noticed as associate editor of JVP is that reviewers are 
growing less patient with phylogenetic analyses that do not address the 
specimens themselves, and which instead code taxa from publications. This is 
being viewed increasingly as unacceptable, and I wholeheartedly embrace that 
view. It's the specimens that are our primary data."

I completely agree that the specimens are our primary data and that coding from 
specimens is preferrable to any other resource.  When I was younger back in 
2000 and such, I would picture a paleontologist poring over a specimen in his 
hands, turning it this way and that under the light, only to triumphantly type 
a 0 or 1 into Nexus Data Editor and move on to the next character.  If only the 
world were so kind.  The dirty truth is that this is generally not the way 
things work, and indeed can't be, given financial and business considerations.

Any decent cladistic analysis needs a large number of taxa, and for most 
analyses this means specimens will be spread over the world.  For the original 
TWG analysis of Norell et al., seeing all the relevent specimens would mean 
going to the AMNH, BMNH, BPM, BSP, BYU, CEU, CMN, DINO, FMNH, GMV, HMN, IGM, 
IVPP, JM, LH, MNU, MOR, MUCP, NGMC, PIN, PVPH, ROM, RTMP, UA, UCMZ, USNM, WDC, 
YPM and ZPAL collections.  China, Mongolia, Russia, Argentina, Poland, England, 
Spain, Germany, Canada and over ten states of the US.  If you're lucky, you'll 
see the specimens on a traveling exhibit (with the caveat it usually makes them 
harder to examine up close) or on loan to another museum.  Many museums have 
casts, but these are of varying quality.  Realistically, very few 
paleontologists are going to have the resources to see all the specimens.  
Travel cost is simply too high.

But people do manage to travel, and many papers indicate specimens were 
consulted for coding.  I myself visited the AMNH twice, and they happened to 
have many IGM specimens at the time as well.  When I write my papers, I'll put 
down my reference for Saurornithoides as "AMNH 6516".  But the truth is my 
codings don't come from looking at the specimen in person.  I saw it, I held 
it, sure.  But when you visit a museum collection, you get 6 hours or so per 
day, since they're only open for so long.  And there are usually several 
revelent specimens in a museum, sometimes an extremely large number (AMNH, IGM, 
IVPP, MOR, RTMP, etc.).  Moreover, there are usually rules about removing only 
one specimen from cabinets at a time, filling out cards to replace them in the 
meantime, etc..  And you want to be careful, since nobody wants to be "the one 
who dropped Ornitholestes' skull".  If I were to try to code Ornitholestes for 
the TWG matrix while looking at it in the AMNH collections, it would near 
certainly take my entire time for that day and more.  Any good matrix has at 
least a couple hundred characters, often several hundred.  It takes time to 
code.  And while people have the resources to visit museum collections, I 
highly doubt most have the resources to return every day for a week or two.  
And realistically, matrices aren't made by having a list of characters, and 
running through them for every taxon, a taxon at a time.  Often comparing taxa 
will lead to new interpretations (as in my last blog post on therizinosaur 
accessory trochanters) or a taxon's morphology will lead you to redefining your 
states or adding a new character.  Who's going to go back to New York to see if 
Ornitholestes has more than ten maxillary teeth after they've rewritten their 
character to be "11 or more teeth" instead of "9 or more"?  And once you have a 
new/revised matrix several years down the line, and new taxa have been 
discovered, are you supposed to go on your whorlwind worldwide tour again?  
Curators can do these things for specime!
ns in the
o live by a museum or have specimens on loan to them, but nobody can do them 
for the majority of specimens.

So how do people "code from specimens"?  They take photos.  Lots of photos.  
And they code from those.  They're often better than the literature because 
they're in color and from as many angles as you want, but with the internet 
publication quality is improving.  There would be almost no reason to see 
Australovenator for myself, for instance, since Hocknull et al. did such a good 
job of photographing it.  There are certainly things photographs don't show 
well- sutures and restoration on some specimens, depth of depressions, some 
texture.  But these are hardly numerous enough to justify hundreds of dollars 
to see yourself.  "The literature" has gotten a bad name, but its photos can be 
just as good as your own, and its descriptions are usually written by people 
with as much or more knowledge and experience as you.  This is good news for 
all of us though, since it means anyone can have access to the same resources 
the professionals use for most specimens, without travel costs.  The internet's 
gone a long way to providing a Shiny Digital Future for publication access, but 
I think we could do more. 

What if there was an online database of specimen photos, in high resolution 
color, that anyone could access?  The museums' permission would be needed of 
course, and undescribed specimens could be excluded if under study, but it sure 
beats everyone spending their resources to photograph the same things.  It's 
also better than the current situation where people have photos of poorly 
described specimens, but aren't allowed to distribute them, even if they've 
been in the literature for over a decade and have no plans for redescription.  
The odd thing is, a person is generally allowed to travel to the collection and 
take their own photos, but not recieve or distribute those which have already 
been taken.  I don't want people to think I'm just bitter about lacking access 
myself, as there are plenty of specimens I have photos of (both taken myself 
and kindly provided by others) and aren't allowed to distribute.  So I'm on 
both sides.  But surely such a system is broken when we're witholding 
information from each other that we could get for hundreds of dollars in travel 
fees and won't be redescribed soon anyway. 

I'd be willing to throw my (distributable) photos into such a project if 
someone were to set it up.  The primary obstacle besides getting museum 
permission would be the huge storage space, but it could probably even be done 
on Flickr or Picasa.  What does everyone think?

Mickey Mortimer
The Theropod Database- http://home.comcast.net/~eoraptor/Home.html