Handling Casts in Paleo data

[Jegelewicz]

Let's talk about stuff that isn't "real"! The Alabama collection has a cast of the British Museum's Archaeopteryx (Cool!), but I am struggling with how to catalog it. I want to hang on to the identification so that it can be found in taxonomic searches, so I first thought I would identify it as Archaeopteryx and use the part name "cast, reproduction" with "skeleton" in the comments, but that seems bad for finding "all Archaeopteryx skeleton casts" as the comments are free text. So if I use the part name "skeleton", I could put "cast" in part condition, but that puts me in the same boat.

There are other casts in the collection of "4th vertebra" and such, so I think that holding on to part names that don't include "cast" is important, but it is also important to identify the casts as such.

I am considering a part preservation attribute of "reproduction" - an imitation, transcript, or copy of an original object (such as a fossil, letter, or painting)

So for the Archaeopteryx cast I would have:

Identification = Archaeopteryx part name = skeleton part preservation = reproduction

Does that sound like a good way to handle stuff like this? @dperriguey @mbprondzinski @AJLinn @dustymc

[mbprondzinski]

I like that or facsimile.

From: Teresa Mayfield-Meyer [mailto:notifications@github.com] Sent: Friday, February 08, 2019 3:24 PM To: ArctosDB/arctos Cc: Prondzinski, Mary Beth; Mention Subject: [ArctosDB/arctos] Handling Casts in Paleo data (#1912)

Let's talk about stuff that isn't "real"! The Alabama collection has a cast of the British Museum's Archaeopteryx (Cool!), but I am struggling with how to catalog it. I want to hang on to the identification so that it can be found in taxonomic searches, so I first thought I would identify it as Archaeopteryx and use the part name "cast, reproduction" with "skeleton" in the comments, but that seems bad for finding "all Archaeopteryx skeleton casts" as the comments are free text. So if I use the part name "skeleton", I could put "cast" in part condition, but that puts me in the same boat.

There are other casts in the collection of "4th vertebra" and such, so I think that holding on to part names that don't include "cast" is important, but it is also important to identify the casts as such.

I am considering a part preservation attribute of "reproduction" - an imitation, transcript, or copy of an original object (such as a fossil, letter, or painting)

So for the Archaeopteryx cast I would have:

Identification = Archaeopteryx part name = skeleton part preservation = reproduction

Does that sound like a good way to handle stuff like this? @dperrigueyhttps://github.com/dperriguey @mbprondzinskihttps://github.com/mbprondzinski @AJLinnhttps://github.com/AJLinn @dustymchttps://github.com/dustymc

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[dustymc]

part preservation = reproduction

I have no better ideas, and that should be easy to recover if someone has a better idea in the future.

letter, or painting

No objections, but please make sure (documentation) that doesn't blur over into part name "media."

[Jegelewicz]

OK, thanks! This is how I will handle these. @dustymc can you delete the part "cast, reproduction"? I think that is is redundant given this treatment and could cause confusion.

[AJLinn]

I'll think about this - I like it in principle. I just had to look up this category of items for a colleague in our education collection. Most of our items have ID names that contain "replica". (https://arctos.database.museum/saved/Replicas) We'll probably continue to follow our naming convention, but we could use the part preservation = reproduction as another way to find them.

[dperriguey]

This might be an issue somewhere else on our github, but why are there no mold options for parts? We have cast, but no mold.

And I'd only use reproduction if it was actually reproduced. Sometimes you're out in the field and you can't take the whole outcrop with you, sad face...tear. So, you make a mold of the fossil you can't take out of the outcrop, bring that back and give it a number. We have a few of these as well as some number of fossil molds.

[dustymc]

actually reproduced

I think what you describe is not made by nature==>reproduced, no? Ideally you'd just have two events - one collection (where "collecting" is making the mold) and one manufacture (so it's obvious you made the mold in the field).

@Jegelewicz I deleted cast, reproduction

[dperriguey]

Yes I mean manufactured, not made by nature; the molds made by the collector.

Any thoughts on molds made in nature?

[dustymc]

molds made in nature

They're just parts.

mold-->made by natural processes mold+reproduction-->made by people

[dperriguey]

No, there is not a part name mold in Arctos.

[dperriguey]

I'm sorry, I was not explicit. There is a part name cast in Arctos, no part name mold. Two different things but closely related.

[dustymc]

Ah...

What do you call them in your collection? Seems like the original part would be more useful. "Mold" (or cast) is just about useless - "skull" (or whatever) + some_part_attribute=mold/cast+(when relevant) some_part_attribute=reproduction would be more accessible data - can we go in that direction?

"unknown" + some_part_attribute=mold/cast should work if you're making/finding casts of random things for some reason - which is about what the current 87 casts look like....

[dperriguey]

I understand the point of utility you're making. Lots of the stuff we are putting in Arctos are ID'd already. I don't want the volunteers or other employees making judgment calls yet; I need time to teach them. Otherwise they are just entering things without acknowledging the parts (entering in everything as shell (fossil) to get the count of specimens in). I would like to teach them the ability to say this is a mold, this is a cast, this is a body fossil etc. The complex stuff is left to me (identifying things) and somewhere else down the line when someone looks at a specimen and makes changes to it's record (re-identification).

In the field and in identifications post field work we call things body fossils, casts or molds, or trace fossils/ichnofossils it is specific to the preservation. That is, the preservation of evidence of life in the geologic record.

I cannot call a cast by it's original part because there are no original parts. I could say cast of the entire animal or partial cast naming the anatomical character. Today I found an internal cast (some shell bits left on the outside). I was able to identify it by it's general morphology and those bits of shell left. The adductor scars of the bivalve were preserved. I noted this in my ID remarks. I'm taking this to be along the lines of your part attribute formulas above?

Does this help?

[dustymc]

There's always some way of saying "we don't know (much)" and I don't think it's ever a bad thing to use it when you don't know. "Probably a clam" (ID=Mollusca ?) and "I don't really know what to call this thing, but I'm going to stick a barcode on it so we can find it later" (part=unknown) is a really useful first step. For other material, or the vague stuff after having been reviewed by multiple experts, we might get to a specific part name ("shell") and something about how it's "preserved" (mold). I don't see any reason not to limit parts to parts and preservation to preservation.

A cast isn't exactly a shell, but that still seems like a useful viewpoint - people working on shell morphology might want to find it and not find the casts of other stuff.

That should work for any precision from a lump of maybe-interesting rock possibly having some sort of association with some sort of animal cataloged by a brand new student, to a very specific part analyzed by a whole string of experts, and make the data from both ends of the spectrum very searchable.

If users really don't ever care what a cast is of, then "cast" might make a good part name. That seems unlikely to me, but ??

[dperriguey]

I think I understand this point. From my point of view we have more specific terms for the part of traces (casts and molds are in reality only traces just very specific traces). You can make a mold from a cast, a cast from a mold. If I have a bivalve and it is a cast, it is assumed that it is an external cast. That is, some external morphological characteristics are preserved from the bivalve. Logically, these came from "shell." There are external molds where a negative impression is preserved (you can fill it in and make a replica of the actual shell). Now there are what are called internal casts (steinkerns) that preserve the internal characteristics (mold) of the animal's shell.

For a dino print, it is usually an external mold (except for situations when it's not). You can fill it in and make a replica of the actual foot.

I definitely care if I'm doing a morphological analysis of whether specimens are traces or body fossils. If you're doing a trace fossil study, cool to use the casts and molds. If you're doing some hardcore morphological analysis and taxonomic study, you probably don't want to publish with traces in your analysis. Oh, but wait: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906676/

This explains pretty well: https://en.wikipedia.org/wiki/Trace_fossil_classification

[dperriguey]

I would still like a mold part, if that is possible?

[dustymc]

So part "mold" (and cast) would be used for molds of everything from leaves to T. rex skulls? That seems unnecessarily sloppy to me, but if that's how things are cataloged then I suppose it's what we should do.

@KatherineLAnderson your opinion on this would be appreciated.

[dperriguey]

Because "parts" have a natural anatomical component as their definition for Arctos, right? If that's the case, cast, mold, and trace fossil shouldn't be in there. This is a type of preservation not anatomy. More specifically, a type of fossilization process is necessary as well.

I agree that not sticking to anatomical parts is sloppy. So lets keep part anatomical and mode of preservation for fossils a necessary addition to Arctos.

[campmlc]

Should we add the case, cast, mold, trace etc terms to part attributes as a preservation type? Also fossilization terms?

On Tue, Feb 19, 2019 at 1:19 PM dperriguey notifications@github.com wrote:

Because "parts" have a natural anatomical component as their definition for Arctos, right? If that's the case, cast, mold, and trace fossil shouldn't be in there. This is a type of preservation not anatomy. More specifically, a type of fossilization process is necessary as well.

I agree that not sticking to anatomical parts is sloppy. So lets keep part anatomical and mode of preservation for fossils a necessary addition to Arctos.

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[Jegelewicz]

Because "parts" have a natural anatomical component as their definition for Arctos, right?

No - ethnology and art collections will catalog other things, but perhaps in the biological world this should be true.

These terms seem useful:

Cubichnia are the traces of organisms left on the surface of a soft sediment. This behaviour may simply be resting as in the case of a starfish, but might also evidence the hiding place of prey, or even the ambush position of a predator. Domichnia are dwelling structures that reflect the life positions of organisms, for example the subsurface burrows or borings of suspension feeders, and are perhaps the most common of the established ethological classes. Fodinichnia are feeding traces which are formed as a result of organisms disturbing the sediment in their search for food. They are normally created by deposit feeders as they tunnel through soft sediments, usually producing a 3D structure. Pascichnia are a different type of feeding trace for which the trophic guild responsible are grazers. They create 2D features as they scour the surface of a hard or soft substrate in order to obtain nutriment. Repichnia are locomotory tracks that show evidence of organisms moving from one station to another, usually in a near-straight to slightly curved line. Most of the very few traces to be verifiably assigned to a specific organism are in this category, such as various arthropod and vertebrate trackways.[3]

should they be the "parts" we have in fossil collections when anatomy doesn't apply?

[dustymc]

Parts are physical things. Taxon names (I believe all of those thing in your list are) are concepts. There's an easy separation in biology - we have a liver (part) and it's from a woodrat (name). One is pretty useless without the other, unless you want to trust us on the "Occurrence" for which we have no evidence and use it in range maps or something. The separation isn't so distinct in cultural collections - we have a teapot (part; physical item; thing to which one could apply a barcode) and it's called a teapot (maybe with some qualifiers or something). They generally use "object" for parts - I don't think we lose anything since the part would share the string with the ID, and it saves introducing infinite parts.

That does seem a bit towards the cultural item end of the spectrum. If you have a Repichnia then you automagically know something about the part - it's some sort of goo-turned-rock that's capable of preserving trackways, or a reproduction of that. From that viewpoint, "cast" (or mold) may make sense as a part name.

For http://arctos.database.museum/guid/DMNS:Mamm:8257, I don't think cast makes much sense. It's a reproduction (man-made I presume, but those data belong elsewhere) of a bit, and it could be a LOT of bits. People looking at seal flipper morphology don't want it. People looking at brain morphology might. It's not discoverable except by searching remarks, which isn't controlled. Is that the same sort of material as http://arctos.database.museum/guid/MVZ:Mamm:117883 (remark=cranial endocast)? Maybe...

[Jegelewicz]

If you have a Repichnia then you automagically know something about the part - it's some sort of goo-turned-rock that's capable of preserving trackways, or a reproduction of that.

If you had an ID of "Dimetropus", wouldn't a part of Repichnia make sense? I mean, the definition sounds like a part to me:

Repichnia are locomotory tracks that show evidence of organisms moving from one station to another, usually in a near-straight to slightly curved line. Most of the very few traces to be verifiably assigned to a specific organism are in this category, such as various arthropod and vertebrate trackways

[KatherineLAnderson]

If you have a Repichnia then you automagically know something about the part - it's some sort of goo-turned-rock that's capable of preserving trackways, or a reproduction of that.

If you had an ID of "Dimetropus", wouldn't a part of Repichnia make sense? I mean, the definition sounds like a part to me:

Repichnia are locomotory tracks that show evidence of organisms moving from one station to another, usually in a near-straight to slightly curved line. Most of the very few traces to be verifiably assigned to a specific organism are in this category, such as various arthropod and vertebrate trackways

Repichnia is an ichnotaxa (identification) so it shouldn't be used as a part name.

I think having a preservation attribute would be great with options like cast (ie: replica), natural cast (ie: cast made by nature), external mold, internal mold, and other terms already discussed here. UAMES has been including preservation as condition (part "exoskeleton", condition "external mold"; or part "trace fossil", condition "natural cast", remark "tridactyl dinosaur track") but a preservation attribute would be a welcome improvement.

As for part names of ichnofossils, I think "trace fossil" is a broad but sufficient part name. It describes what the object is. If we want to keep part names strictly anatomical, it won't work because ichnofossils/trace fossils are not anatomical (a footprint is "anatomical" in some sense but not in the same sense as a metatarsal, and a burrow is not anatomical at all)--they are a record of behavior that is preserved.

[dustymc]

If we want to...

"We" just want to record data in such a way that users (including "us") can find what they want to find.

"Surely the paleontologist have this all figured out!"

• Gordon, ca. 2003, as our experiment with hierarchical parts was dying of a tragic overexposure to reality.

I was hoping nobody would notice the logical conclusion when my little thought experiment is applied to burrows! ("Whole organism"?!?)

So,

• keep "trace fossil"
• add preservation terms
• drop part 'cast'

Part=unknown, preservation=[replica/natural] cast is a direct replacement for the current data, in which we just record "cast" (or mold). If we know more (eg, it's a cast of a femur), there's a place for that information. "Tridactyl dinosaur track" (and anything else that can't be made by combining ~existing parts and the "preservation" terms above) still gets stuffed into remarks.

Reasonable/workable??

[dperriguey]

Preservation mode as in permineralization (petrification), carbonaization, recrystallization, original shell/bone (this one is weird and we should not debate it we see this in say Cretaceous bivalves that have original aragonite shell or with hominin remains), or replacement. Trace fossils are preserving either anatomy/morphology or behavior. This is usually just sediment infilling and removal of the body fossil.

-keep "trace fossil" - remove cast (we can not it in remarks if that makes it searchable for someone looking for/excluding casts or molds)

-collection mode (replica/natural) or something else that makes more sense

-add preservation terms listed above

[Jegelewicz]

All sounds reasonable to me! Thank you so much @KatherineLAnderson

One item - @dperriguey by collection mode, do you mean collecting method (which I believe is free text) or collecting source (as in "wild caught", etc.)?

I do think we may need a new collecting source for paleo stuff. "wild caught" works, but is a little misleading?. I have been using it for stuff that was dug up and "captive" for man-made casts, but I'm not sure that makes sense to any outside of Arctos people and maybe doesn't make sense internally either....

[dustymc]

"wild caught"

Yea that's a horrible term. It usefully means something like "useful for distribution maps." New Issue...

[mbprondzinski]

I would not consider that apropos. How about “exhumed” In place of “wild caught”

From: Teresa Mayfield-Meyer [mailto:notifications@github.com] Sent: Thursday, February 21, 2019 10:24 AM To: ArctosDB/arctos Cc: Prondzinski, Mary Beth; Mention Subject: Re: [ArctosDB/arctos] Handling Casts in Paleo data (#1912)

All sounds reasonable to me! Thank you so much @KatherineLAndersonhttps://github.com/KatherineLAnderson

One item - @dperrigueyhttps://github.com/dperriguey by collection mode, do you mean collecting method (which I believe is free text) or collecting sourcehttp://arctos.database.museum/info/ctDocumentation.cfm?table=CTCOLLECTING_SOURCE (as in "wild caught", etc.)?

I do think we may need a new collecting source for paleo stuff. "wild caught" works, but is a little misleading?. I have been using it for stuff that was dug up and "captive" for man-made casts, but I'm not sure that makes sense to any outside of Arctos people and maybe doesn't make sense internally either....

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[campmlc]

"collected from nature"?

On Thu, Feb 21, 2019 at 9:41 AM Mary Beth notifications@github.com wrote:

I would not consider that apropos. How about “exhumed” In place of “wild caught”

From: Teresa Mayfield-Meyer [mailto:notifications@github.com] Sent: Thursday, February 21, 2019 10:24 AM To: ArctosDB/arctos Cc: Prondzinski, Mary Beth; Mention Subject: Re: [ArctosDB/arctos] Handling Casts in Paleo data (#1912)

All sounds reasonable to me! Thank you so much @KatherineLAnderson< https://github.com/KatherineLAnderson>

One item - @dperrigueyhttps://github.com/dperriguey by collection mode, do you mean collecting method (which I believe is free text) or collecting source< http://arctos.database.museum/info/ctDocumentation.cfm?table=CTCOLLECTING_SOURCE> (as in "wild caught", etc.)?

I do think we may need a new collecting source for paleo stuff. "wild caught" works, but is a little misleading?. I have been using it for stuff that was dug up and "captive" for man-made casts, but I'm not sure that makes sense to any outside of Arctos people and maybe doesn't make sense internally either....

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[Jegelewicz]

1942

1943

Please comment there.

[Jegelewicz]

also see https://github.com/ArctosDB/new-collections/issues/170#issuecomment-453298901

[Jegelewicz]

See also https://github.com/ArctosDB/arctos/issues/1943#issuecomment-466483018

[Jegelewicz]

Moved this back from documentation-wiki because I need clarification.

Here is what I suggest we do. All based upon this: https://sciencing.com/types-fossils-formed-8035701.html and comments here

Remove from Parts:

cast

Add to parts:

• fossil cast - formed by mineral deposits into the mold left by rotting organic material, resulting in a three-dimensional replica of the hard structures of a plant or animal
• fossil mold - formed when a plant or animal decays completely but leaves behind an impression of itself, like a hollow mold; no organic material is present and the organism itself is not copied
• fossil imprint - found in silt or clay, like the mold or impression fossils, but they leave behind just a two-dimensional imprint
• trace fossil - evidence of either anatomy, morphology, or behavior left in soft sediment which has hardened to become sedimentary rock

Add to preservation attributes

• permineralization - each part of the organism is replaced by minerals, leaving a stone copy of the organism
• carbonization - conversion of organic matter into carbon through destructive distillation
• recrystallization - need definition

Sorry to re-hash, but I couldn't get a cohesive concept out of all the above discussion. @mbprondzinski @dperriguey @KatherineLAnderson @Nicole-Ridgwell-NMMNHS

[Nicole-Ridgwell-NMMNHS]

Technically, fossil cast, fossil mold, and fossil imprint are types of preservation. I think it would be better to put them under preservation attributes? For example, you could have a trace fossil that is also a fossil mold (ex. the mold of the inside of a burrow, a natural mold of a track).

We should also separate fossil mold into fossil internal mold and fossil external mold.

permineralization - each part of the organism is replaced by minerals, leaving a stone copy of the organism

definition should be - pores of the original tissues are filled with mineral deposits

recrystallization - need definition

definition is - original minerals in the skeletal tissues converted into a new crystal structure.

We also need to add replacement and original tissue

Replacement - Original tissue is replaced with minerals from the surrounding water and sediment Original Tissue - Fossil specimens which have not been mineralized and the original tissue has not been significantly chemically altered

Another that may need to be added is Petrifaction. Petrifaction is a combination of permineralization and replacement. It is very common (i.e. petrified wood).

[Jegelewicz]

@Nicole-Ridgwell-NMMNHS I originally had those as preservation, but couldn't decide for sure - you have made it clear for me!

I'll get to adding this stuff to the code tables...

[Jegelewicz]

We should also separate fossil mold into fossil internal mold and fossil external mold.

@Nicole-Ridgwell-NMMNHS how would the definitions for these two differ?

Currently I have:

fossil mold - formed when a plant or animal decays completely but leaves behind an impression of itself, like a hollow mold; no organic material is present and the organism itself is not copied

[Jegelewicz]

@dustymc how many parts of "cast" are currently in Arctos and at which institutions? I'd like to proceed with moving those to "trace fossil" and adding the appropriate preservation attribute as this might take some time for collections to sort through if there are a lot.

Thanks!

[dustymc]

I think many of these are NOT fossils - they're reproductions of modern bones-n-stuff.

I think a cast/mold of a track/burrow/etc. IS a trace fossil (with some preservation data) and a cast/mold of a skull/shell/etc. is NOT a trace fossil.

UAM@ARCTOS> select guid_prefix, count(*) from collection, cataloged_item,specimen_part where collection.collection_id=cataloged_item.collection_id and cataloged_item.COLLECTION_OBJECT_ID=specimen_part.derived_from_cat_item and part_name='cast' group by guid_prefix;

GUID_PREFIX                            COUNT(*)
------------------------------------------------------------ ----------
UTEP:Mamm                                 1
DMNS:Mamm                                 1
UNM:ES                                   21
UCM:Fish                                  1
UTEP:HerpOS                               1
MVZ:Bird                                  3
UCM:Herp                                 19
MVZ:Mamm                                 56
MVZ:Herp                                  1
UCM:Mamm                                  2

10 rows selected.

[mbprondzinski]

This muddies the water more, I must say... https://en.wikipedia.org/wiki/Trace_fossil_classification

[Jegelewicz]

I think a cast/mold of a track/burrow/etc. IS a trace fossil (with some preservation data) and a cast/mold of a skull/shell/etc. is NOT a trace fossil.

YES! Documentation started: http://handbook.arctosdb.org/how_to/How-To-Catalog-Fossil-Material.html

[KatherineLAnderson]

I think many of these are NOT fossils - they're reproductions of modern bones-n-stuff.

I think a cast/mold of a track/burrow/etc. IS a trace fossil (with some preservation data) and a cast/mold of a skull/shell/etc. is NOT a trace fossil.

Yes. That is correct. I wouldn't map what is labeled as part=cast to part=trace fossil for that reason. Otherwise all of this is sounding great.

[KatherineLAnderson]

This muddies the water more, I must say... https://en.wikipedia.org/wiki/Trace_fossil_classification

Yes, but this is a muddy-ing of identification rather than parts.

[Jegelewicz]

cast/mold of a skull/shell/etc.

Recommending that these things should be cataloged as:

part=skeleton, femur, shell, etc. part preservation=reproduction

[mbprondzinski]

I actually had a dream about this last night...I concur! "Recommending that these things should be cataloged as:

part=skeleton, femur, shell, etc. part preservation=reproduction"

[Jegelewicz]

I actually had a dream about this last night.

Yes, I've got you dreaming about Arctos.....

[mbprondzinski]

Yes, I've got you dreaming about Arctos.....

I know...sick, isn't it?!

[Nicole-Ridgwell-NMMNHS]

We should also separate fossil mold into fossil internal mold and fossil external mold.

@Nicole-Ridgwell-NMMNHS how would the definitions for these two differ?

Currently I have:

fossil mold - formed when a plant or animal decays completely but leaves behind an impression of itself, like a hollow mold; no organic material is present and the organism itself is not copied

fossil external mold - formed when a plant or animal decays completely but leaves behind an external impression of itself, like a hollow mold; no organic material is present and the organism itself is not copied

fossil internal mold - formed when a plant or animal is filled in with sediment and then decays completely, leaving behind an internal impression of itself; no organic material is present and the organism itself is not copied

[Jegelewicz]

Thanks @Nicole-Ridgwell-NMMNHS !

Added as: fossil mold, external - formed when a plant or animal decays completely but leaves behind an external impression of itself, like a hollow mold; no organic material is present and the organism itself is not copied

fossil mold, internal - formed when a plant or animal is filled in with sediment and then decays completely, leaving behind an internal impression of itself; no organic material is present and the organism itself is not copied

this way they will sort more appropriately.

[Nicole-Ridgwell-NMMNHS]

@Jegelewicz

fossil imprint - found in silt or clay, like the mold or impression fossils, but they leave behind just a two-dimensional imprint

Somehow I missed before that we're using 'fossil imprint' instead of 'compression fossil', which is the technical term. Fossil imprint is not a technical term and could be defined in many ways.

[Jegelewicz]

@Nicole-Ridgwell-NMMNHS how about:

fossil, compression = found in silt or clay, like the mold or impression fossils, but they leave behind just a two-dimensional imprint

[Jegelewicz]

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctpart_preservation#fossil__compression

I think we are done here.