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Mickey Mortimer | 1 Jun 2011 04:03
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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
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Jaime Headden | 1 Jun 2011 05:13
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RE: The myth of coding from specimens firsthand and the untapped resource of photos


  Let me get this argument out of the way first:

  If you had the opportunity to either study from the specimen, or study from a photograph, would you chose
the latter? A good deal of investigation cannot actually be done by visual examination from a flat photo,
as you say it obscures the third-dimensional quality the object confers. Photos + casts help ameliorate
this problem, but does not substitute the original. The worst downside of photographic examination is
that detailed "invasive" techniques, such as computed tomography scanning, absolutely require
physical handling, and cannot be done any other way. Brochu's experience is derived almost immediately
after detailed work from scanning croc and a tyrannosaur skull, and doing a large portion of his work
picking apart the ct-slices, so we should forgive him his blunt attitude.

  While a photographic database is _helpful_, it should never be _preferred_, but even more preferential
would be a three-dimensional digital database, but this requires hundreds of thousands of man-hours
work scanning relevant and secondary specimens. Then there's the exponentially more difficult task of a
CT database. The time to prepare the photographic database would be long, and costly, and certainly
involve massive amounts of patience, and in a time of economic floundering, when the US at least has been
cutting back its "discretionary" science spending and certain vociferous factions antithetical to
Science have risen up (especially in connection to "ClimateGate"), most researchers opting to take
personal projects on should have to shoulder the burden of their desires. Any further in
 crease in the quality of virtual data as a resource takes time and money, and we can spend that either
travelling to the sources, or paying for the sources to develop resources to negate that.

Cheers,

Jaime A. Headden
The Bite Stuff (site v2)
http://qilong.wordpress.com/

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)
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evelyn sobielski | 1 Jun 2011 05:18
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AW: The myth of coding from specimens firsthand and the untapped resource of photos


> 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?

I'd completely support such work, though my contributions typically would have skin and feathers still
attached (of these I have a few 100s already; if the opportunity exists I tend to photo anything that might
be interesting and often the specimens next to it too). Crown Theropoda bones might be of interest to many
paleontologists however, and I presume I'll be seeing quite a lot of these (Recent and fossil) in the next years.

Such a database would also be an invaluable aid in the digitization of specimens. I have noted that e.g.
GBIF, but also similar databases, have a major problem with accuracy and nonverifiability of label
information (e.g. "S[an]" misread and databased as "South"). Label photos would completely solve this
problem. To think further, the public at large could thus assist with databasing collections,
decreasing the cost for collecting institutions (which may be prohibitive, at about 1 US$/€ per
speimen in a 100% in-house approach). You may have noted that reCAPTCHA is already being exploited by
spammers. Transcription of handwriting as CAPTCHA will be somewhat tougher to program than for printed
text, but it can be done, and handwriting recognition is something that AI algorithms are likely 
 to fail at routinely for a long time to come.

Does a good online howto for osteological specimen photography exist for cases where ammonium chloride is
not an option?

Thanks in advance,

Eike
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Mickey Mortimer | 1 Jun 2011 05:52
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RE: The myth of coding from specimens firsthand and the untapped resource of photos


As I specifically stated "I completely agree that the specimens are our primary data and that 
coding from specimens is preferrable to any other resource", I don't you why you bothered to ask the
question or restate that photos should never be preferred.  I also noted that photos aren't good at
providing some kinds of data, but this is a small minority of the kind of data we code in matrices.  My point
was that while photos are not ideal, they are what we have to work with the majority of the time, simply due to
how the world works.  If the worst downside of photos is that we can't use CT scanning on them, then that's
not much of a downside at all since A. extremely few specimens of anything have been CT scanned, and B. we
already have a database for that- Digimorph.  I don't see how it "would be long, and costly, and certainly
involve massive amounts of patience" to set up a photo 
 database.  We all have the photos on our hard drives already.  We set up a free photo hosting account
online and upload them, which the websites even let us do in bulk.  The most tedious part would be labeling
the photos and getting a museum's permission, but that seems like a small price to pay for what we gain. 
Just because something isn't the ideal solution in a perfect world with no constraints on time, distance
or money doesn't mean it shouldn't be pursued.

Mickey Mortimer

----------------------------------------
> Date: Tue, 31 May 2011 21:13:57 -0600
> From: qi_leong <at> hotmail.com
> To: mickey_mortimer111 <at> msn.com; Dinosaur.Mailing.List <at> listproc.usc.edu
> Subject: RE: The myth of coding from specimens firsthand and the untapped resource of photos
>
>
>   Let me get this argument out of the way first:
>
>   If you had the opportunity to either study from the specimen, or study from a photograph, would you chose
the latter? A good deal of investigation cannot actually be done by visual examination from a flat photo,
as you say it obscures the third-dimensional quality the object confers. Photos + casts help ameliorate
(Continue reading)

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Tim Williams | 1 Jun 2011 08:37
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Re: Parahongshanornis, new Chinese Cretaceous bird (free pdf)

David Marjanovic <david.marjanovic <at> gmx.at> wrote:

> Interesting that *Parahongshanornis* retains two phalanges in the 3rd
> finger.

The major manual digit of _Patagopteryx_ has three phalanges (with the
third phalanx being ungual-like) and is also quite long.  It'd be
interesting to see a biomechanical study done on _Patagopteryx_, to
ascertain if this flightless bird had the potential for two-handed
grasping.  The forelimbs of _Patagopteryx_ are not that reduced - much
less so than alvarezsaurids and hesperornithids.  Relative to hindlimb
length, they are about double the length of compsognathid forelimbs.

> *Parapropalae(o?)hoplophorus*.
>
> I'm not kidding.

No, I believe you.  When a fossil is christened was an inventive,
imaginative or even humorous name, it engenders more interest in the
actual fossil.  Names like _Parahongshanornis_ disappear without
trace.  But names like _Tyrannosaurus_ ("tyrant lizard"),
_Brontomerus_ ("thunder-thighs"), _Pulchrapollia_ ("pretty Polly"),
_Seimosaurus_ ("earthquake lizard"), _Diabloceratops_ ("devil horned
face") or _Shaochilong_ ("shark-toothed dragon") take on a life of
their own.  People will remember the name _Beelzebufo_ (a prehistoric
frog) long after they've forgotten _Sineoamphisbaena_ (a purported
fossil amphisbaenian).  Even relatively prosaic names like
_Haplocheirus_ and _Caudipteryx_ are original, instead of just tacking
'Para' or 'Eo' or 'Pro(to)' on to an existing genus name.
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Heinrich Mallison | 1 Jun 2011 09:23

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

I fully agree that it is always the specimen one SHOULD code from.
I also agree that in the time of decreasing funding and increasing
quality of photographs a digital database accessible to all is the
best alternative.

For me, the most problematic issue here seems to be copyright. Until
thjat is sorted out the utility of a database will be very limited.

Therefore, I can only recommend publishing in open-access journals
that allow unlimited, high-resolution color figures. Palaeontologia
Electronica comes to mind.

(Full disclosure: I am a style editor at PE)

:)
Heinrich
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Mike Taylor | 1 Jun 2011 09:38
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Specimen photography guide (Was: The myth of coding from specimens firsthand and the untapped resource of photos)

On 1 June 2011 04:18, evelyn sobielski <koreke77 <at> yahoo.de> wrote:
> Does a good online howto for osteological specimen photography exist for cases where ammonium chloride
is not an option?

Well, there is this tutorial on SV-POW!:
http://svpow.wordpress.com/2010/02/12/tutorial-how-to-photograph-big-bones/

Though it doesn't touch on the problems of photographing SMALL bones
for obvious reasons.
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Mike Taylor | 1 Jun 2011 09:43
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Re: The myth of coding from specimens firsthand and the untapped resource of photos

Mickey, your plan is a good one.  Yes, of course, seeing specimens in
person is best; and no, of course it isn't always possible.  Sharing
digital photographs would be a very useful step in a good direction,
and the technology is definitely there.  I don't even think it needs
much space in the scheme of things -- a few gigabytes goes a long way.
 You should definitely resist scope-creep: people will suggest (and
rightly) that it would cool to add surface scans, and CT-cross
sections, and histo slices, and so on; but what's cool can be an
impediment for actually getting stuff done.  Just a freely browsable
gallery of photos would be a huge win.

BTW., I've made a (very small) contribution in this direction: photos
of the holotypes of my babies Xenoposeidon and Brontomerus are
available here:
        http://www.miketaylor.org.uk/dino/xeno/extras.html#3
        http://www.miketaylor.org.uk/dino/brontomerus/extras.html#3

-- Mike.

On 1 June 2011 04:52, Mickey Mortimer <mickey_mortimer111 <at> msn.com> wrote:
>
> As I specifically stated "I completely agree that the specimens are our primary data and that
> coding from specimens is preferrable to any other resource", I don't you why you bothered to ask the
question or restate that photos should never be preferred.  I also noted that photos aren't good at
providing some kinds of data, but this is a small minority of the kind of data we code in matrices.  My point
was that while photos are not ideal, they are what we have to work with the majority of the time, simply due to
how the world works.  If the worst downside of photos is that we can't use CT scanning on them, then that's
not much of a downside at all since A. extremely few specimens of anything have been CT scanned, and B. we
already have a database for that- Digimorph.  I don't see how it "would be long, and costly, and certainly
involve massive amounts of patience" to set up a phot
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David Marjanovic | 1 Jun 2011 10:09
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Re: Parahongshanornis, new Chinese Cretaceous bird (free pdf)

> > Interesting that *Parahongshanornis* retains two phalanges in the
> > 3rd finger.
>
>  The major manual digit of _Patagopteryx_ has three phalanges (with
>  the third phalanx being ungual-like) and is also quite long.

That's the 2nd finger. That's normal.

I agree, though, that somebody should do a biomechanical study of the 
forelimbs of *Patagopteryx* (which I'm not confusing with *Patagonykus* 
this time).
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David Marjanovic | 1 Jun 2011 10:17
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Re: The myth of coding from specimens firsthand and the untapped resource of photos

>  The time to prepare the photographic database would be long, and
>  costly, and certainly involve massive amounts of patience, and in a
>  time of economic floundering, when the US at least has been cutting
>  back its "discretionary" science spending and certain vociferous
>  factions antithetical to Science have risen up (especially in
>  connection to "ClimateGate"), most researchers opting to take
>  personal projects on should have to shoulder the burden of their
>  desires. Any further increase in the quality of virtual data as a
>  resource takes time and money, and we can spend that either
>  travelling to the sources, or paying for the sources to develop
>  resources to negate that.

What is cheaper: an institution paying for having its collections 
photographed, or the same institution paying its researchers to zoom 
around the globe again and again?

I bet it's the former by an order of magnitude or two.

The need to travel around the globe to see specimens will not disappear; 
but if we can restrict it, while at the same time _decreasing_ our 
dependence on crappy line drawings, that's exactly what we should do.
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