Dear Colleagues, So I’ve been wondering whether to wade into this issue.. There seems to be an undercurrent here of mathematics vs biology, but I suspect that the real issue here is probably morphometric theory versus the pragmatic compromises necessary when using morphometric tools to answer biological questions. Others on this thread have thought (and written) much more deeply about the interface of morphometric theory and biology than I have, but for what it’s worth, here are my two cents on this issue. Fundamentally, what is most important is that quantifications of morphology capture relevant biological variation while avoiding artifacts that can skew or mislead interpretation. That matters much more to than whether there is real homology or not. I'm not even sure what "real homology" for landmark coordinate data means in a biological sense, even for Type 1 landmarks. The "identity" or homology of landmarks tends to become messy pretty quickly when the underlying developmental biology is examined closely. I think Paul O'Higgins gave a great talk once on that basic theme if I remember correctly. Chris Percival also did a nice analysis showing how apparently obviously homologous landmarks that occur at intersections of major components of the face can drift in terms of the origin of the underlying tissue during development. So, I think we may sometimes get too hung up on this ideal that the points that we place on morphological structures actually represent something real. They are simply intended to quantify morphology within the context of a biological question. It's not landmarks but rather the patterns of variation that an analysis generates are the objective basis of study and those patterns are only objective within the context of a biological question. The key issue is avoiding artifacts that can influence biological interpretation. In terms of this discussion, clearly semi-landmarks present one kind of challenge where one has to be careful about artifacts. Another, perhaps more currently relevant challenge, however, is the quantification of variation in volumetric images or surfaces that have been nonlinearly registered to an atlas. In this case, one can place landmarks anywhere and recover the corresponding location in every specimen or image. That correspondence is a sort of homology and those landmarks are not slid around like semi-landmarks. However, they are not placed by an observer as distinct observations either. These kinds of points behave fairly similarly to manually placed points (albeit without measurement error and with artifacts that appear as one tries to register increasingly dissimilar shapes). However, I think that, driven by the needs of the biological questions, we are increasingly going to be using this kind of automated quantification of morphology in morphometric analyses, so we need to think carefully about how to validate such data. My own bias here is that appropriate validations address how well (and this can be defined contextually) such quantifications measure the biological effects of interest rather than how well they simulate the behavior of manually placed landmarks. I suppose this is an argument for biological pragmatism, but I hope some find this useful. Benedikt -Original Message- From: Adams, Dean [EEOBS] Sent: Wednesday, November 7, 2018 6:48 AM To: andrea cardini ; firstname.lastname@example.org Subject: RE: [MORPHMET] Re: semilandmarks in biology Folks, I think it is important to recognize that the example in Andrea’s earlier post does not really address the validity of sliding semilandmark methods, because all of the data were simulated using isotropic error. Thus, the points called semilandmarks in that example were actually independent of one another at the outset. Yet a major reason for using semilandmark approaches is the fact that points along curves and surfaces covary precisely because they are describing those structures. Thus, this interdependence must be accounted for before shapes are compared between objects. The original literature on semilandmark methods makes this, and related issues quite clear. What that means is that evaluating semilandmark methods requires simulations where the points on curves are simulated with known input covariance based on the curve itself (difficult, but not impossible to do). But using independent error will not accomplish this. The result is that treating fixed landmarks as semilandmarks can lead to what some feel are unintended outcomes, just as treating semilandmarks as fixed points are known to do (illustrated nicely in Figs 1-4 of Gunz et al. 2005). But both are mis-applications of methods, not indictments of them. As to the other points in the thread (the number of semilandmark points, etc.), earlier posts by Jim, Philipp, and Mike have addressed these. Dean Dr. Dean C. Adams Director of Graduate Education, EEB
*Dennis Slice is the 2017 recipient of the Rohlf Medal for Excellence in Morphometric Methods and Applications * Over the course of three decades Dennis E. Slice, Professor of Scientific Computing at Florida State University (Tallahassee), has contributed in many crucial ways to the development, dissemination and innovative application of today's best morphometric methods. His early articles and reviews helped teach biologists about Procrustes analysis and its differences from other approaches beginning well before his actual doctorate was awarded. More recently, he and his students have advanced novel landmark-free methods for analysis of 3D image data with important applications in areas such as forensic anthropology that academic biologists rarely explore. Along the way, he has developed 20 open source software packages that are widely used for morphometric analysis across the full range of his application fields. Slice’s contributions to the dissemination of morphometric methods include influential surveys, edited volumes, and symposia. Particularly important are the dozens of courses and scores of workshops through which he has expanded our morphometrics community. Another major contribution is his commitment to the continuing advancement of this community's collective skills and influence through his expansion and moderation of the community's main web-based news outlet and question forum, Morphmet. Slice’s work has expanded the range of valid applications of morphometric methods. His extensive publication record includes innovative and diverse applications of morphometrics in, among other fields, orthodontics, evolutionary biology, biomedical engineering, paleoanthropology, evolutionary psychology, protective clothing design, and marine biology. His funding sources are likewise diverse, ranging well beyond the usual list of sponsors of basic research to such institutions as the National Institute of Justice and the U. S. Army. The 2017 Rohlf Medal will be presented to Prof. Slice on October 24, 2017 at Stony Brook University. Afterwards, he will present a lecture (title to be announced). Previous recipients of the Rohlf Medal are Fred Bookstein (University of Vienna), Paul O'Higgins (University of York), and Benedikt Hallgrimsson (University of Calgary). Click here <http://life.bio.sunysb.edu/morph/RohlfMedal/travel.html> for notes on travel and accommodations if you plan to attend. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
*2017 CALL FOR NOMINATIONS* *The Rohlf Medal* The Rohlf Medal was established in 2006 by the family and friends of F. James Rohlf to mark his 70th birthday. He has been a longtime Stony Brook University faculty member and is currently Emeritus Distinguished Professor in the Department of Ecology and Evolution, and Research Professor in the Department of Anthropology. Recipients of the Rohlf Medal will be recognized for excellence in their body of work on the development of new morphometric methods or for their applications in the biomedical or biological sciences, including evolutionary biology, population biology, physical anthropology, developmental biology, neurobiology, computer sciences and medicine. The term ‘morphometrics’ is intended to include high-dimensional pattern analyses of biological shape, especially those that analyze shape in a comprehensive way, or of covariation of shape with other variables. The award can recognize advances in the mathematical or statistical theory underlying morphometric methods, new software that implements or visualizes new methods, or specific new biological findings that rely crucially on contemporary morphometric methods and represent major advances. Candidates for the Rohlf Medal may be self-nominated or nominated by others. They must possess a Ph.D. degree or the equivalent. The winning candidate must agree to attend the award ceremony in person in order to accept the Rohlf Medal and then deliver the award lecture. Nomination packages should include, (1) a description of the body of work (not to exceed two pages) on which the candidacy is based, (2) reprints of no more than three relevant papers and/or software products, (3) a curriculum vitae, and (4) three letters of support. Nominating packages should be uploaded to the Rohlf Medal website (http://life.bio.sunysb.edu/ee/rohlf_medal/apply.html) and received by 5 pm, EST, 15 July 2017 to be assured of full consideration. The successful candidate will receive the Rohlf Medal and a cash prize at Stony Brook University, planned for October 24th, 2017. She or he will deliver a lecture that is appropriate for a broad audience, ranging from the exact sciences to the humanities, concerning the morphometric methodology, software, or findings for which the Rohlf Medal was awarded. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org. 2017-Rohlf Medal Call for Nominations Final.docx Description: MS-Word 2007 document