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One small step for digital Palaeontology

The time of digital technology is upon us. No scientific domain is embracing it’s fast-paced and dynamic progression more so than Palaeontology. One such realm that is exploding with new studies and enrapturing the minds of people and the global media is the increasing possibility to digitise and manipulate three-dimensional fossils. Surface laser-scanning, C-T scanning and mechanical digitizers are all commonplace now in palaeontological studies. The implications of such techniques are far-reaching, from reconstructing robotic dinosaurs (see video), to understanding vertebrate biomechanics at an intricate level. Other palaeontologists digitally reconstruct the internal anatomy of various organisms; for example, in the Herefordshire deposits in the UK, digital models are recreated from exquisitely preserved fossils within nodules to look at the evolution of the internal structures  that were pivotal in the evolution of extant hyperdiverse invertebrate groups, such as arthropods.

It is pretty well established that the fossil record is fraught with completeness issues. I covered the problem of this in a previous post in terms of understanding biodiversity patterns in deep geological time, in the context of lineage completeness. Another problem however is individual specimen completeness. Several authors have attempted to compensate for this secondary level of ‘bias’, using various quantitative metrics, and use these to guide assessments of biodiversity through time in specific lineages (e.g., sauropod dinosaurs). Another problem is that often, fossils have been ‘squished’ and distorted by the weight of successive layers of rock over the thousands or millions of years they have been buried for. This is a problem which is typically found in dinosaur skulls, making them somewhat resemble Imhotep in The Mummy (this may be fictional).

Imhotep is pissed
Ugly beyond all reason, possibly as a result of post-mortem decay. "You talking to me?!"

Geometric morphometrics is something that I’ve mentioned in previous posts. It sounds awful, the  very mention of it usually enough to put people off or smash a keyboard upside your head. But thanks to several review papers, the basic concepts are now much easier to grasp and apply to a variety of scientific hypotheses. Statistics are quantitative, easy to record, less subjective than qualitative statements, and available for repeated manipulation through a wide variety of methods. The integration of geometry-based analysis is now commonplace in almost every aspect of Palaeontology, intimately coupled with an increase in the availability of digital techniques. The fact that you don’t have to damage unique specimens during the processes (usually) is a bonus too!

The latest analysis, and a critical study for palaeontologists and museum curators around the world, uses geometry-based reconstruction of a poorly-preserved fossil to digitally reconstruct missing or distorted parts. And the best part about it, is that it’s fully open access (including all supplementary videos); the comment that “this method does not require specialised software or artistic expertise” is perhaps a bit misleading, as you firstly need a fossil and a CT scanner (or a previous scan), a pretty beasty PC, and the software mentioned is hardly cheap (Rhinoceros is €195 for a student license, and for Geomagic the cheapest price I could find was $8000). The actual software used (Mimics) appears to be free, but I’m still awaiting confirmation for downloading. Additional software, such as MeshLab and Autodesk Maya are freeware, at least for trial versions.

Clack et al. set out to build a method of digital reconstruction that builds upon previous methods, giving greater geometric accuracy. The methods revolve around using a digital mesh obtained through laser or C-T scanning as a model for a landmark-based geometric reconstruction. The sample specimen is a vertebra from the infamous tetrapod fossil Acanthostega. Only one half of the vertebra is actually preserved, therefore this was digitally reconstructed and attached to its mirror image, creating a bilaterally symmetrical three-dimensional element.

Landmark selection involved a mixture of Type 1 and Type 2 landmarks; that is topographically homologous points, mixed with sites of geometric significance, such as local maxima or minima of curvature. These were used as the basis for constructing a surficial grid of contour lines describing the medial and lateral geometry of the neural spine. Videos of the processes involved are actually available online, embedded within the article, a really awesome and useful addition, making the whole methodology more transparent and easier to replicate, should you wish. There’s not really much else to say about the methodology; the processes, such as modelling and surface extrapolation are laid out systematically and reasonably easy to understand for anyone with an understanding of the concepts of geometry and fossils.

The resultant reconstructions are high quality, smooth and geometrically faithful in representing the original vertebra in three dimensions, free of any taphonomic deformation or distortion, and with missing parts accurately reproduced. The groups of models created are validated using Procrustes superimposition and principal components analysis, two standard statistical techniques. The first two principal components do appear to have a low explanatory power however (PC-1 = 24.3%), which may be an issue relating to the complexity in the form of the vertebra. The authors are right to discount the use of the thin-plate spline technique, as this is known to be misleading in that the deformation patterns it produces are homogeneous with respect to the landmark configuration, leading to potentially false morphological variation in areas of no data, something which is largely overlooked.

Acanthostega model reconstruction, half-fish half-muppet; Copyright - Eliot Goldfinger

The advantages of the techniques explored here are in the handling style of the models, and their statistical power and accuracy. Furthermore, anyone can conduct or replicate these methods, providing they have access to an initial CT scan. The potential applications are numerous too: digital models of reconstructed elements can give more accurate parameters for biomechanics where data may have been previously extrapolated in a subjective or qualitative manner; it may yield hitherto unknown data for character construction, which may in turn increase the validity of phylogenetic analysis. The landmark mapping procedure may need refinement in terms of increasing the number of points, such as by using semi-landmarks, which will more accurately reconstruct the surface geometry and open the way for other statistical procedures.

The study represents a great step forward though in accurate specimen reconstruction, and reveals another field in which the power of geometric morphometric techniques is unparalleled. A limitation could be that to reconstruct missing parts, you have to have an idea of what the gross geometry is, meaning at least one half of a bilaterally symmetrical element must be present. This means that if you wanted to reconstruct the neural spine for example, it would be impossible if the whole part was absent, even if the entire centrum was preserved. This is something that could be integrated in future using close relatives of the species that are being reconstructed.

0 thoughts on “One small step for digital Palaeontology

  1. The low score of the principal component axes could well represent the fact that the measurements are independant one from another and express different aspects of the morphology, rather than a general deformative trend.

  2. Great post, as always, Jon. It all kinda reminds me of what Gould said in his 1991 paper on the BG arthropods. Forgive me for quoting pretty liberally my favourite bits,

    The vague concept of evolutionary “relationship” includes both cladistic (branching order) and phenetic (morphological distance) components; and these are not the same, either logically or empirically. A major triumph of evolutionary studies in our generation has been, through the development of cladistics, the codification of a methodology for objective definition and determination of branching order. (The soundness of the logic does not guarantee a resolution in every, or even in most, cases; for our world of rampant homoplasy and imperfect data often frustrates hope for confident answers.)

    Success often breeds both overconfidence and overextension. Many evolutionists, intoxicated
    with the victory of cladistics in its own sphere, have assumed that it must represent a panacea for all questions about “relationships.” […]

    The phenetic question of defining a morphospace and mapping the distribution of actual organisms is much more difficult than the cladistic problem of determining branching order. Branching order unfolds in Newtonian time and in a space even simpler than Euclid’s-the two-dimensional world of Abbott’s Flatland. A morphospace, on the other hand, is not only richly multidimensional but seemingly idiosyncratic for each kind of organism. How can it be defined with anything like the rigor of cladistic space and time? In the light of this frustrating difference between rigor for branching order and verbal vagueness for morphospace, who can blame critics for their lack of sympathy with the phenetic question? Bengtson (1990: p. 115) referred to the notion of body plans as “a seedy concept if there ever was any”; while
    Fortey (1989: p. 303) wrote: “The problem with ‘disparity’ is that its estimation depends on
    the authority of the expert: how is he to know what makes-what is ‘worth’-a phylum? Or what a class?”

    We cannot assuage this frustration by importing a logically inappropriate technique like cladistics. The resolution can only arise within the structure of phenetic methods. Either we develop a set of quantitative techniques for the definition and differential filling of morphospace, or we are condemned to vagueness.

    What, then, do we need? Not simply a good method for the multivariate description of organisms, for such we have (Sneath and Sokal 1973; Bookstein 1977a,b). And not even a
    proper multivariate description of morphological transformation-whether by D’Arcy Thompsonian (1917) coordinate transformations, Huxleyan (1932) allometric growth gradients,
    or more modern methods like trend surface analysis (Sneath 1967). We need, instead, to define a full range of the abstract (and richly multivariate) space into which all organisms may fit (the morphospace). We must then be able to characterize individual organisms and plot them within this encompassing space. Finally, we need to measure density, range, clumping, and a host of other properties that determine differential filling of this totality; and we must be able to assess the variation in this differential filling through time. […]

    These questions are dauntingly difficult, and I do not pretend to have a solution. […]

    I do confess some fears that, in toto, the question of morphospace may be logically intractable,
    not merely difficult. Consider the two obvious impediments: (1) All successful methods of comparison (from transformed coordinates by Albrecht Diirer to modern factor analysis) work with homologous points. How can differences be quantified if such points of comparison do not exist. Is a coral more different from an oak tree than a cow? What is the distance between a rock and a hard place? Between Scylla and Charybdis? (2)How can an objective morphospace be determined if organisms have infinite numbers of potential characters? We are not, after all, simply placing creatures into an exterior and objective Euclidian world. We are defining their morphospace in terms of their characters. Such issues may make a general solution intractable. We may not be able to answer, with satisfying rigor, the question of whether mammals evolve faster than clams: for how can teeth be compared with pallial sinuses? But science usually proceeds by resolving smaller puzzles and then moving on toward more general formulations. We should be able to establish adequate morphospaces for creatures with comparable body plans and joint possession of sufficient homologies. […]

    I have written this paper because I believe that the question of defining morphospaces and mapping their differential filling through time is so vital to our understanding of life’s history, particularly to the potential contribution of paleontologists. Yet relatively little has been done in this area, despite promising starts, and despite a near assurance that smaller subdivisions of the problem are tractable (for creatures with sufficient homology), whatever the status of the full generality. I believe that a serious attack on this problem would be well worth the concentrated attention of paleontologists with quantitative skills and evolutionary interests. Usually, when we are stymied in science, our impediment lies with missing data, thus breeding frustration; for, in such an empirical field, supply of absent data often involves an inevitable component of waiting and hoping. But, in the case of morphospace and its differential filling,
    we face the much happier and resolvable issue of abundant data waiting for a technique.

    I would say that, with digital morphometrics, finally we have the technique that Gould was waiting for. A long time coming, though!

    1. I meant BS – Burgess Shale btw. And here’s a citation for the Gould paper, if you wanted it,

      Gould, S.J. “The Disparity of the Burgess Shale Arthropod Fauna and the Limits of Cladistic Analysis: Why We Must Strive to Quantify Morphospace.” Paleobiology (1991): 411–423.

  3. Jon,
    I appreciate your interest in pterosaurheresies.com and I recognize your potential by the way you’ve handled your own blog and the subjects therein. I’m very impressed and expect great things from you as time goes by.

    Dave

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