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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@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 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@hotmail.com
>> To: mickey_mortimer111@msn.com; Dinosaur.Mailing.List@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 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 
>> 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.
>>
>> Cheers,
>>
>> Jaime A. Headden
>> The Bite Stuff (site v2)
>> http://qilong.wordpress.com/
>>
>> "Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)
>>
>>
>> "Ever since man first left his cave and met a stranger with a
>> different language and a new way of looking at things, the human race
>> has had a dream: to kill him, so we don't have to learn his language or
>> his new way of looking at things." --- Zapp Brannigan (Beast With a Billion 
>> Backs)
>>
>>
>>
>>
>>
>> ----------------------------------------
>> > Date: Tue, 31 May 2011 19:03:47 -0700
>> > From: mickey_mortimer111@msn.com
>> > To: dinosaur@usc.edu
>> > Subject: 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 
>> > speci!
>> me!
>> > 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
>> >
>>
>
>
>