Morphometrician of the Month (April)

This month we would like to introduce a new shape-lover, friend, and future collaborator Dr. Robert Z.(Zac) Selden Jr. from the crhr:archaeology

photo

Name: Dr. Robert Z. Selden Jr.

E-mail: selden3d@gmail.com

Institution: Stephen F. Austin State University

What is your research on?

Geometric morphometrics of ceramic vessels, Caddo ceramics primarily, but I am also engaged in a bit of an affair with projectile points (less Paleoindian, and more Archaic). I’m interested in assemblage-level variation in ceramic shape and size (to include decorative elements) as these elements may help us to further extend our archaeological inferences related to cultural transmission, craft theory and the—potential—identification of communities of practice.

I see promise in the capacity of geometric morphometrics to assist in identifying specific vessels that might represent the beginning (or end) of a morphological tradition. While I don’t subscribe to evolutionary archaeology, my perhaps-too-lofty goal is to eventually identify (to the extent possible) the ceramic equivalent of a transitional species.

image 1

Network of ceramic types (circles/nodes) plotted by archaeological sites (lines/edges) within the study area. If there is an edge (or multiple edges) between two nodes, they both appear at the same (or multiple) site(s). If two or more types appear at multiple sites, the lines/edges between them are larger (weighted).

Upon completion of the quantitative analysis, shape attributes are ascribed qualitative identifiers (vessel shape numbers) based on the outcome of the analysis, which are used in a network analysis.

In practice, I use those data garnered from the integrated approach of geometric morphometrics and network analyses as something akin to a hypothesis engine, where the results of the analyses (which can—and should—be viewed independently of one another) tend to generate more questions than they answer. At the end of each run, I spend time reflecting on the process, and the method, while writing like a madman (I have dozens of journals full of observations, notes and possible future projects at this point), as I try to capture inferences and ancillary observations from each cycle before moving on to the next.

image 2

The same network as above, but with shape numbers added. The different colours represent different communities (defined by modularity) in which more/less vessel shapes are associated with each of the ceramic vessel types. I am currently working to plot these spatially and temporally (using R) to see how they articulate with known Caddo periods and phases.

Those questions raised—at least in part—in each iteration are helping me to refine and redress additional ancillary observations like vessel tilt and rotational asymmetry, along with a host of others. Over the past year (the last six months in particular), I have spent a lot of time on Skype asking folks whether they are seeing the same thing as I am. Many of the ancillary observations look to be quite useful, and I want to ensure that we capitalize on each of them as time comes available.

image 3

Rotational asymmetry – where the widest vessel radius is rotated 360-degrees to generate a nominal surface that is contrast with the mesh to calculate (and illustrate) the deviation from rotational symmetry—a.k.a., asymmetry. Note: I have shifted to a new method for the formal asymmetry analysis (more on that below), but this method may be useful in finally quantifying the differences for rotational asymmetry between coil-built and wheel-built vessels (where wheel-built vessels are generally thought to be more symmetrical).

What got you into morphometrics?

The genesis of my interest in geometric morphometrics began at a pub with my graduate school roommate (imagine that), who is a biological anthropologist. He was (is, rather) using geometric morphometrics to look at a variety of biological structures (from ape jaws to rodent post-crania), and we began a discussion of how the various methods might be applied to ceramics to answer questions related to cultural transmission.

image 4

Results of assemblage-level variation in vessel shape from three Caddo sites.

At that time, I had been working to insert myself between the repatriation and reburial process for Caddo burial vessels; particularly those that fell under the purview of the Native American Graves Protection and Repatriation Act (NAGPRA), as I wanted to document these important cultural items before they were no longer available for study. It was at this point that I really began contemplating the potential contributions of geometric morphometrics to my current research design. However, the bulk of our discussions remained centred upon how to properly identify landmark and semi-landmark data points on a series of specimens that—for all intents and purposes—have only a single homologous landmark (the central base), which made me question whether this was even feasible.

https://sketchfab.com/models/42620534f6384e36b61728467367e190/embed

CNO 3SV10 81-89-1
by Dr. Robert Z. Selden Jr.
on Sketchfab

 

Where would you insert landmarks and semi-landmarks on the vessel above? This is an interactive 3D image; press play to activate it, then click/drag to rotate.

At this point, I want to echo Professor Collard’s statement from Morph2015, in that I see one of the principal challenges of employing a study of geometric morphometrics in archaeology as defining homologous (or for that matter, even semi-homologous) landmarks. It took me quite a while to settle on my current method of applying landmark and semi-landmark data points to the sample of 3D ceramics.

Initially, we used Cartesian coordinates that were subjectively applied, then exported those to Morphologika for analysis. While I was pleased to have taken a first stab at geometric morphometrics, I would be remiss if I didn’t mention my disappointment at the lack of replicability that I came to see as blatantly obvious in the pilot study.

In its current form (see an example in the YouTube video below), my method for applying landmark/semi-landmarks to ceramics has evolved substantially (after dozens of iterations), and continues to be refined. I have also shifted over to the geomorph package in R for the analysis.

YouTube video that outlines the process used to populate landmark/semi-landmark data points on a ceramic vessel using reference geometry in Geomagic Design X.

Subsequent to alignment, I now use Geomagic Design X (reverse-engineering software) to insert a revolving vector (defined by an algorithm—not subjectively [although note that the algorithm is still representative of a bias; just not my own]), then the single landmark (the only homologous point that I see as transcending all of the various vessel classifications [bowl, bottle, etc.]) at the central base, now defined by projecting a single point at the intersection of the 3D mesh and the revolving vector.

The basal plane (defined during alignment) is used to orient the vessel as if it were sitting on a planar surface—like the ground—which I assume to be the intent of the maker. This plane serves as the basis for a mesh sketch, used to generate and extrude a cylindrical surface around the circumference of the vessel. Deviations are calculated between the cylindrical surface and the mesh, making it possible to identify (consistently – ergo, replicable) the widest point of each vessel. That point is then used to insert a plane—coplanar to the central vector—along the widest profile of the vessel (defined by that widest point on the mesh surface).

The plane inserted along the widest profile is used as the base plane for a 3D mesh sketch, where 12 splines (six full vessel profiles) are inserted at equidistant intervals around the circumference of each vessel. Those splines are cut at the point of highest curvature along the rim. As an aside, I want to mention here that one of my goals was to generate a landmark/semi-landmark configuration that I could use for both 2D and 3D data, since we have hundreds of images in publications that can (and will) augment this initial study. The splines on the interior of the vessels were deleted (primarily because I use surface scanners, and cannot scan the interior of carinated bowls, bottles, etc.), and equidistant semi-landmarks were inserted along those splines from the central base (LM1) to the highest point of curvature on the rim along each radius, while rotating the vessel in a clockwise direction (although see note below). Once populated, those data are then exported to a .csv file.

Note: I have since incorporated a minor alteration to this method, and am now splitting each of the splines at the base/body and body/lip junctures as well. This provides a means by which I can explore the correlation between the base, body and lip, and explore things like shifts in basal morphology through time (which turned out to be important—remember those ancillary observations?). Additionally, I can use those divisions to figure out which component best discriminates between the various vessel shapes.

From this point, you’re likely familiar with the remainder of the analytical process – import raw data to your favourite software, then dig in.

image 5

Another quick note here – I am now using those landmarks associated with the widest vessel profile (a) to look at variations in (b) fluctuating and (c) directional asymmetry. I think that both measures of asymmetry have some potentially interesting applications in archaeology (for a variety of artefact classes—certainly not limited to ceramics).     

Do you have any advice for budding morphometricians/shape-lovers?

Ask questions – lots of them, and be skeptical of your own work. Also, be comfortable enough in your own skin to genuinely laugh at your mistakes, shake them off, and keep failing forward. I used to skateboard when I was younger, and still remember one of my best friends telling me, “if you’re not falling, you’re not pushing yourself hard enough.” I think that the same logic applies here (but do yourself a favour and try to do your falling in the lab, rather than in print—so, full-circle back to my initial answer; ask lots of questions).

Some of my biggest gains have come from posting my ideas online and soliciting feedback from the larger community of practitioners. Join the MORPHMET list, and participate in discussions about topics or concerns that interest you. Also try to think through issues that others are having; it helps to conceptualize the process outside of those artefacts or specimen categories that you become comfortable with.

What is your go-to guide/article?

It’s not a guide or an article, but a rather short read that I think many of you would enjoy; The Shape of Time by George Kubler. If I find myself discouraged, or feeling stagnant, this gets me right back into the swing of things. Also, if you have not read The Writing Life by Annie Dillard, you should. Plenty of guidance in there that can be appreciated by graduate students and professionals alike—truly transcen­ds disciplines.

Favourite software?

I’m a really big fan of geomorph. I had been working with Emma Sherratt for about a year before heading to Portugal last fall for a workshop with Dean Adams, Michael Collyer and Antigoni Kaliontzopoulou. These folks have been absolutely wonderful, and I cannot thank them enough for their guidance and support as I have made my way through the various analyses.

Favourite online reference (besides this)?

I always have one eye on the geomorph blog, and frequently find myself checking the new meetings, workshops, courses, etc. page on the SUNY Stony Brook website.

Additionally, I assembled the beginnings of what I’m hoping will be a nice crowdsourced bibliography of geometric morphometric resources—for archaeology and beyond—beginning with Sarah and Christian’s list, then expanding on it a bit (access that here—generate a .pdf of the bibliography by clicking on “PDF” at the top of that screen, and please share widely), and I’m hoping that this community will help me to get this resource up to date. Send additional references to selden3d@gmail.com with Morph2016 as the subject line (include DOI and ISSN where possible), and I’ll get them added!

Many thanks to Sarah and Christian for putting this resource together for the archaeological morphometric community. It’s nice to see more folks beginning to work through and apply these methods to archaeological problems.

^C&S

Morph2016 Workshop!

Shape-lovers,

We can now announce that in conjunction with Morph2016 (https://morph2016.wordpress.com/) and The Natural History Museum we will be organising a one-day workshop providing an introduction to geometric morphometrics for archaeologists and anthropologists.

Led by Prof. Norman MacLeod (The Natural History Museum, UK) this one-day workshop will provide a theoretical and practical overview of geometric morphometrics, from data collection, and choosing the right software, to data analysis and presentation. There will also be opportunities throughout the day to discuss your own data, should you wish to receive feedback, in addition to other techniques.

During the extended lunch there will also be an opportunity to visit the NHM anthropological and archaeological collections (I KNOW, RIGHT!?). More details about this will be outlined in due course.

The workshop will take place on 25th May 2016 (the day before Morph2016). Spaces are limited to 40 people so please do register as soon as possible, shape-lovers.

More information can be found on our Eventbrite page:

http://www.morph2016workshop.eventbrite.co.uk/

This will be a great opportunity to get a hands-on experience of GM before Morph2016. We hope to see many of you there!

^C&S

giphy
               What a time to be alive. (Source: GIPHY)

 

 

 

Morphometrician of the Month (March)

We are pleased to announce a new series here at Archaeomorph called the ‘Morphometrician of the Month’. Each month we will post a short interview with a morphometrician from varying backgrounds and academic levels to highlight the application of geometric morphometrics in their research.

We are happy to announce Dr. Tim Astrop as our first Morphometrician of the Month and are looking forward to working with him in our future Archaeomorph collaborations.

Profile

Name: Dr. Tim Astrop

E-mail: tia20@bath.ac.uk

Institution: The University of Bath

Academic level: Postdoctoral Research Associate

What is your research on? Currently, I am engaged in a project looking at extinction selectivity in ammonites. As a palaeobiologist I’m interested in what we can learn about life on earth from it’s extensive, rich and (in my opinion) undervalued fossil record. Basically, ammonites were around for 350 million years and survived several major mass extinctions, even the Permo-Triassic extinction which saw the demise of an estimated 96% of all marine species. Somehow these tenacious little molluscs survived. Often as single lineages and despite losing much of their morphological disparity to such catastrophic events, they quickly radiated in their aftermath, evolving similar morphologies again and again. We are interested in elucidating which, if any, morphological and functional features certain lineages possessed that would enable them to survive or conversely, set them up for extinction. I currently use 3D rapid prototyping technology alongside 2D geometric morphometric methods to study the iconic shells of the group and subject them to both simulated and experimental water-flow experiments to see how form affected function (in terms of stability/drag etc).

morph of the month 1

Favourite software? I’m a superfan of Geomorph, the R package by Dean Adams and Em Sherratt. It is amazingly multi-functional and has the capability to capture and analyze 2D and 3D morphometric data in a plethora of ways. More recently I’ve been playing with Momocs, another R package that performs some really funky 2D outline analyses and produces some amazing graphical displays of your data.

Favourite online reference (besides this)? The Geomorph package website: http://geomorphpackage.blogspot.co.uk/ it has loads of info, tutorials and Em Sherratt is amazingly responsive to queries and ideas regarding the package and it’s development.

If you are interested in being our Morphometrician of the Month please contact archaeomorph@gmail.com.

^C&S

Statistical Support Group for Archaeologists

Shape-lovers,

Over the next few months (i.e. for the foreseeable future) both of us here at ArchaeoMorph will be hosting a series of internal statistical support sessions, here at the University of Southampton (Department of Archaeology), specifically aimed towards archaeologists of all years, covering everything from arithmetic means to canonical variates.

We will advertise all support sessions over this, and the Twittersphere, including dates of our drop-in data cafe sessions, and our program workshop days.

All are invited! For those who are unable to make it to these sessions: fret not! We will upload all our PowerPoint presentations to our ArchaeoMorph forum, including archaeological datasets we will use.

Today we hosted our first session (thank you to all those that attended!), providing a general introduction to statistics for archaeologists including: 1) hypothesis construction, independent/dependent variables, graphical representations of data and descriptives (dispersion, shape, central tendency). This IS now live on the forum.

Stay tuned!

^C & S

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Navigating the bridge of archaeology together…

 

 

Good news ! (JAS and Morph2016)

Good news shape-lovers!

Following the success of Morph2015 we can announce that our special issue proposal for the Journal of Archaeological Science has been accepted. Titled ‘Deriving meaning from metrics: examining geometric morphometric frameworks within archaeological analyses‘ the edited volume will provide a review of how archaeologists are using geometric morphometric methodologies, and most importantly, the future of the methods within various sub-categories of archaeology.

Guidelines for authors will be forwarded on this week; if this is something you would like to contribute to then please contact us ASAP with a working title, and an abstract (C.Hoggard@soton.ac.uk/S.Y.Stark@soton.ac.uk).

Also, have you heard about Morph2016!?

The second Morph conference ‘Morph2016: Morphometric Applications in Archaeology and Anthropology’ will be held on the 26th May 2016, and hosted by those amazing shape-lovers at University College London. More details including the CfP and registration can be found here: https://morph2016.wordpress.com/ and their Twitter and Eventbrite pages (@Morph2016 , Eventbrite). In conjunction with the conference we will be hosting a one-day workshop (woohoo!) with Prof. Norman MacLeod in the Natural History Museum (more details to follow this week!). We know how much effort team UCL are investing into MORPH2016 so please do support your fellow shape-lovers!

I’m sure you’ll agree with us that this is an exciting time for studies involving geometric morphometrics within archaeology.

 

giphy 2
Our own version of this will follow shortly… (fundraisergrrl.tumblr.com)

^C & S

UPDATE: Redesigned and with a forum!

Shape-lovers,

We’re now pretty! Over the last few weeks we here at ArchaeoMorph have redesigned the format of the website to what we hope, you think, is a much more suitable and professional design (because we are professionals, right?).

We’ve also added the forum (http://archaeomorph.boards.net/), and we will be continuously updating this in the next few days and from now on. Please do register and contribute; the more people who register, the more effective the forum, the better shape-lover you’ll become!

^C & S

Pretty
Sourced from Giphy (http://giphy.com/gifs/beauty-confidence-selfesteem)