The Legacy of D'arcy Thompson's
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On Genes and Form Enrico Coen*, Richard Kennaway and Christopher Whitewoods
© 2017. Published by The Company of Biologists Ltd | Development (2017) 144, 4203-4213 doi:10.1242/dev.151910 REVIEW On genes and form Enrico Coen*, Richard Kennaway and Christopher Whitewoods ABSTRACT aside ‘not because I doubt for a moment the facts nor dispute the The mechanisms by which organisms acquire their sizes and shapes hypotheses nor decry the importance of one or other; but because we through growth was a major focus of D’Arcy Thompson’s book are so much in the dark as to the mysterious field of force in which the On Growth and Form. By applying mathematical and physical chromosomes lie, far from the visible horizon of physical science, principles to a range of biological forms, Thompson achieved fresh that the matter lies (for the present) beyond the range of problems ’ insights, such as the notion that diverse biological shapes could be which this book professes to discuss (p. 341, Thompson, 1942). related through simple deformations of a coordinate system. However, Much of the darkness and mystery Thompson refers to was lifted in Thompson considered genetics to lie outside the scope of his work, the second half of the 20th century, as the nature of genes and their even though genetics was a growing discipline at the time the mechanisms of action became clear. Nevertheless, the link between book was published. Here, we review how recent advances in cell, gene activity and the generation of form remained obscure, largely developmental, evolutionary and computational biology allow because of difficulties in determining growth patterns and relating Thompson’s ideas to be integrated with genes and the processes them to physico-chemical mechanisms. -
John Wells: Centenary Display Jonty Lees: Artist in Residence Autumn 2005 Winter 2007 6 October 2007 – 13 January 2008
Kenneth Martin & Mary Martin: Constructed Works John Wells: Centenary Display Jonty Lees: Artist in Residence Autumn 2005 Winter 2007 6 October 2007 – 13 January 2008 Notes for Teachers - 1 - Contents Introduction 3 Kenneth Martin & Marty Martin: Constructed Works 4 John Wells: Centenary Display 11 Jonty Lees: Artist in Residence 14 Bernard Leach and his Circle 17 Ways of Looking – Questions to Ask of Any Artwork 19 Suggested Activities 20 Tate Resources & Contacts 22 Further Reading 22 Key Art Terms 24 - 2 - Introduction The Winter 2007 displays present: Kenneth Martin and Mary Martin: Constructed Works (Gallery 1, 3, 4, and the Apse) This exhibition shows the work of two of Britain’s key post-war abstract artists, Kenneth Martin and Mary Martin. The exhibition includes nearly 50 works and focuses on Kenneth Martin’s mobiles and his later Chance and Order series of abstract paintings, alongside Mary Martin’s relief sculptures. Modernism and St Ives from 1940 (Lower Gallery 2) This display of artists associated with St Ives from the Tate Collection is designed to complement the Kenneth Martin and Mary Martin exhibition. It includes work by Mary Martin, Victor Pasmore, Anthony Hill and Adrian Heath alongside St Ives artists such as Peter Lanyon, Terry Frost and Ben Nicholson. John Wells: Centenary Display (The Studio) A small display of paintings and relief constructions by John Wells, designed to celebrate the centenary of his birth. Bernard Leach and his Circle (Upper Gallery 2) Ceramics by Bernard Leach and key studio potters who worked alongside him. These works form part of the Wingfield-Digby Collection, recently gifted to Tate St Ives. -
IV. on Growth and Form and D'arcy Wenworth Thompson
Modified 4th chapter from the novel „Problem promatrača“ („Problem of the observer“), by Antonio Šiber, Jesenski i Turk (2008). Uploaded on the author website, http://asiber.ifs.hr IV. On growth and form and D'Arcy Wenworth Thompson St. Andrews on the North Sea is a cursed town for me. In a winter afternoon in year 1941, a bearded, grey-haired eighty year old man with swollen eyes and big head covered by even bigger hat was descending down the hill side to the harbor. He had a huge butcher’s knife in his hand. A few workers that gathered around a carcass of a huge whale which the North Sea washed on the docks visibly retreated away from a disturbing scene of a tall and hairy figure with an impressive knife. The beardo approached the whale carcass and in less than a minute swiftly separated a thick layer of underskin fat, and then also several large pieces of meat. He carefully stored them in a linen bag that he threw over the shoulder and slowly started his return, uphill. The astonished workers watched the whole procedure almost breathlessly, and then it finally occurred to one of them who was looking in the back of a slowly distancing old man that it was not such a bad idea. It is a war time and shortage of meat. And if professor of natural philosophy Sir D’Arcy Thompson concluded that the fish is edible… Who would know better than him? After all, he thinks only of animals and plants. Of course, Thomson knew perfectly well that the whale is not fish, but to workers this was of not much importance. -
Perspectives
PERspECTIVES steady-state spatial patterns could also arise TIMELINE from such processes in living systems21. The full formalization of the nature of Self-organization in cell biology: self-organization processes came from the work of Prigogine on instabilities and the a brief history emergence of organization in ‘dissipative systems’ in the 1960s22–24, and from Haken who worked on similar issues under the Eric Karsenti name of synergetics11 (TIMELINE). Abstract | Over the past two decades, molecular and cell biologists have made It was clear from the outset that the emergence of dynamical organization important progress in characterizing the components and compartments of the observed in physical and chemical systems cell. New visualization methods have also revealed cellular dynamics. This has should be of importance to biology, and raised complex issues about the organization principles that underlie the scientists who are interested in the periodic emergence of coherent dynamical cell shapes and functions. Self-organization manifestations of life and developmental concepts that were first developed in chemistry and physics and then applied to biology have been actively working in this field19,25–29. From a more general point various morphogenetic problems in biology over the past century are now of view, Kauffman built on the ideas of beginning to be applied to the organization of the living cell. Prigogine and Haken in an attempt to explain the origin of order in biology30–32. One of the most fundamental problems in this complex state of living matter as a self- Self-organization was also invoked to biology concerns the origin of forms and organized end8–10. -
6 Phyllotaxis in Higher Plants Didier Reinhardt and Cris Kuhlemeier
6 Phyllotaxis in higher plants Didier Reinhardt and Cris Kuhlemeier 6.1 Introduction In plants, the arrangement of leaves and flowers around the stem is highly regular, resulting in opposite, alternate or spiral arrangements.The pattern of the lateral organs is called phyllotaxis, the Greek word for ‘leaf arrangement’. The most widespread phyllotactic arrangements are spiral and distichous (alternate) if one organ is formed per node, or decussate (opposite) if two organs are formed per node. In flowers, the organs are frequently arranged in whorls of 3-5 organs per node. Interestingly, phyllotaxis can change during the course of develop- ment of a plant. Usually, such changes involve the transition from decussate to spiral phyllotaxis, where they are often associated with the transition from the vegetative to reproductive phase. Since the first descriptions of phyllotaxis, the apparent regularity, especially of spiral phyllotaxis, has attracted the attention of scientists in various dis- ciplines. Philosophers and natural scientists were among the first to consider phyllotaxis and to propose models for its regulation. Goethe (1 830), for instance, postulated the existence of a general ‘spiral tendency in plant vegetation’. Mathematicians have described the regularity of phyllotaxis (Jean, 1994), and developed computer models that can recreate phyllotactic patterns (Meinhardt, 1994; Green, 1996). It was recognized early that phyllotactic patterns are laid down in the shoot apical meristem, the site of organ formation. Since scientists started to pos- tulate mechanisms for the regulation of phyllotaxis, two main concepts have dominated the field. The first principle holds that the geometry of the apex, and biophysical forces in the meristem determine phyllotaxis (van Iterson, 1907; Schiiepp, 1938; Snow and Snow, 1962; Green, 1992, 1996). -
Copyrighted Material
1 Symmetry of Shapes in Biology: from D’Arcy Thompson to Morphometrics 1.1. Introduction Any attentive observer of the morphological diversity of the living world quickly becomes convinced of the omnipresence of its multiple symmetries. From unicellular to multicellular organisms, most organic forms present an anatomical or morphological organization that often reflects, with remarkable precision, the expression of geometric principles of symmetry. The bilateral symmetry of lepidopteran wings, the rotational symmetry of starfish and flower corollas, the spiral symmetry of nautilus shells and goat horns, and the translational symmetry of myriapod segments are all eloquent examples (Figure 1.1). Although the harmony that emanates from the symmetry of organic forms has inspired many artists, it has also fascinated generations of biologists wondering about the regulatory principles governing the development of these forms. This is the case for D’Arcy Thompson (1860–1948), for whom the organic expression of symmetries supported his vision of the role of physical forces and mathematical principles in the processes of morphogenesisCOPYRIGHTED and growth. D’Arcy Thompson’s MATERIAL work also foreshadowed the emergence of a science of forms (Gould 1971), one facet of which is a new branch of biometrics, morphometrics, which focuses on the quantitative description of shapes and the statistical analysis of their variations. Over the past two decades, morphometrics has developed a methodological Chapter written by Sylvain GERBER and Yoland SAVRIAMA. 2 Systematics and the Exploration of Life framework for the analysis of symmetry. The study of symmetry is today at the heart of several research programs as an object of study in its own right, or as a property allowing developmental or evolutionary inferences. -
Multidimensional Generalization of Phyllotaxis
CYBERNETICS AND PHYSICS, VOL. 8, NO. 3, 2019, 153–160 MULTIDIMENSIONAL GENERALIZATION OF PHYLLOTAXIS Andrei Lodkin Dept. of Mathematics & Mechanics St. Petersburg State University Russia [email protected] Article history: Received 28.10.2019, Accepted 28.11.2019 Abstract around a stem, seeds on a pine cone or a sunflower head, The regular spiral arrangement of various parts of bi- florets, petals, scales, and other units usually shows a ological objects (leaves, florets, etc.), known as phyl- regular character, see the pictures below. lotaxis, could not find an explanation during several cen- turies. Some quantitative parameters of the phyllotaxis (the divergence angle being the principal one) show that the organization in question is, in a sense, the same in a large family of living objects, and the values of the divergence angle that are close to the golden number prevail. This was a mystery, and explanations of this phenomenon long remained “lyrical”. Later, similar pat- terns were discovered in inorganic objects. After a se- ries of computer models, it was only in the XXI cen- tury that the rigorous explanation of the appearance of the golden number in a simple mathematical model has been given. The resulting pattern is related to stable fixed points of some operator and depends on a real parame- ter. The variation of this parameter leads to an inter- esting bifurcation diagram where the limiting object is the SL(2; Z)-orbit of the golden number on the segment [0,1]. We present a survey of the problem and introduce a multidimensional analog of phyllotaxis patterns. -
Theory of the Growth and Evolution of Feather Shape
30JOURNAL R.O. PRUMOF EXPERIMENTAL AND S. WILLIAMSON ZOOLOGY (MOL DEV EVOL) 291:30–57 (2001) Theory of the Growth and Evolution of Feather Shape RICHARD O. PRUM* AND SCOTT WILLIAMSON Department of Ecology and Evolutionary Biology, and Natural History Museum, University of Kansas, Lawrence, Kansas 66045 ABSTRACT We present the first explicit theory of the growth of feather shape, defined as the outline of a pennaceous feather vane. Based on a reanalysis of data from the literature, we pro- pose that the absolute growth rate of the barbs and rachis ridges, not the vertical growth rate, is uniform throughout the follicle. The growth of feathers is simulated with a mathematical model based on six growth parameters: (1) absolute barb and rachis ridge growth rate, (2) angle of heli- cal growth of barb ridges, (3) initial barb ridge number, (4) new barb ridge addition rate, (5) barb ridge diameter, and (6) the angle of barb ramus expansion following emergence from the sheath. The model simulates growth by cell division in the follicle collar and, except for the sixth param- eter, does not account for growth by differentiation in cell size and shape during later keratiniza- tion. The model can simulate a diversity of feather shapes that correspond closely in shape to real feathers, including various contour feathers, asymmetrical feathers, and even emarginate prima- ries. Simulations of feather growth under different parameter values demonstrate that each pa- rameter can have substantial, independent effects on feather shape. Many parameters also have complex and redundant effects on feather shape through their influence on the diameter of the follicle, the barb ridge fusion rate, and the internodal distance. -
A Method of Constructing Phyllotaxically Arranged Modular Models by Partitioning the Interior of a Cylinder Or a Cone
A method of constructing phyllotaxically arranged modular models by partitioning the interior of a cylinder or a cone Cezary St¸epie´n Institute of Computer Science, Warsaw University of Technology, Poland [email protected] Abstract. The paper describes a method of partitioning a cylinder space into three-dimensional sub- spaces, congruent to each other, as well as partitioning a cone space into subspaces similar to each other. The way of partitioning is of such a nature that the intersection of any two subspaces is the empty set. Subspaces are arranged with regard to phyllotaxis. Phyllotaxis lets us distinguish privileged directions and observe parastichies trending these directions. The subspaces are created by sweeping a changing cross-section along a given path, which enables us to obtain not only simple shapes but also complicated ones. Having created these subspaces, we can put modules inside them, which do not need to be obligatorily congruent or similar. The method ensures that any module does not intersect another one. An example of plant model is given, consisting of modules phyllotaxically arranged inside a cylinder or a cone. Key words: computer graphics; modeling; modular model; phyllotaxis; cylinder partitioning; cone partitioning; genetic helix; parastichy. 1. Introduction Phyllotaxis is the manner of how leaves are arranged on a plant stem. The regularity of leaves arrangement, known for a long time, still absorbs the attention of researchers in the fields of botany, mathematics and computer graphics. Various methods have been used to describe phyllotaxis. A historical review of problems referring to phyllotaxis is given in [7]. Its connections with number sequences, e.g. -
Phyllotaxis: a Remarkable Example of Developmental Canalization in Plants Christophe Godin, Christophe Golé, Stéphane Douady
Phyllotaxis: a remarkable example of developmental canalization in plants Christophe Godin, Christophe Golé, Stéphane Douady To cite this version: Christophe Godin, Christophe Golé, Stéphane Douady. Phyllotaxis: a remarkable example of devel- opmental canalization in plants. 2019. hal-02370969 HAL Id: hal-02370969 https://hal.archives-ouvertes.fr/hal-02370969 Preprint submitted on 19 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Phyllotaxis: a remarkable example of developmental canalization in plants Christophe Godin, Christophe Gol´e,St´ephaneDouady September 2019 Abstract Why living forms develop in a relatively robust manner, despite various sources of internal or external variability, is a fundamental question in developmental biology. Part of the answer relies on the notion of developmental constraints: at any stage of ontogenenesis, morphogenetic processes are constrained to operate within the context of the current organism being built, which is thought to bias or to limit phenotype variability. One universal aspect of this context is the shape of the organism itself that progressively channels the development of the organism toward its final shape. Here, we illustrate this notion with plants, where conspicuous patterns are formed by the lateral organs produced by apical meristems. -
Phyllotaxis: a Model
Phyllotaxis: a Model F. W. Cummings* University of California Riverside (emeritus) Abstract A model is proposed to account for the positioning of leaf outgrowths from a plant stem. The specified interaction of two signaling pathways provides tripartite patterning. The known phyllotactic patterns are given by intersections of two ‘lines’ which are at the borders of two determined regions. The Fibonacci spirals, the decussate, distichous and whorl patterns are reproduced by the same simple model of three parameters. *present address: 136 Calumet Ave., San Anselmo, Ca. 94960; [email protected] 1 1. Introduction Phyllotaxis is the regular arrangement of leaves or flowers around a plant stem, or on a structure such as a pine cone or sunflower head. There have been many models of phyllotaxis advanced, too numerous to review here, but a recent review does an admirable job (Kuhlemeier, 2009). The lateral organs are positioned in distinct patterns around the cylindrical stem, and this alone is often referred to phyllotaxis. Also, often the patterns described by the intersections of two spirals describing the positions of florets such as (e.g.) on a sunflower head, are included as phyllotactic patterns. The focus at present will be on the patterns of lateral outgrowths on a stem. The patterns of intersecting spirals on more flattened geometries will be seen as transformations of the patterns on a stem. The most common patterns on a stem are the spiral, distichous, decussate and whorled. The spirals must include especially the common and well known Fibonacci patterns. Transition between patterns, for instance from decussate to spiral, is common as the plant grows. -
Spiral Phyllotaxis: the Natural Way to Construct a 3D Radial Trajectory in MRI
Magnetic Resonance in Medicine 66:1049–1056 (2011) Spiral Phyllotaxis: The Natural Way to Construct a 3D Radial Trajectory in MRI Davide Piccini,1* Arne Littmann,2 Sonia Nielles-Vallespin,2 and Michael O. Zenge2 While radial 3D acquisition has been discussed in cardiac MRI methods feature properties that are particularly well suited for its excellent results with radial undersampling, the self- for cardiac MRI applications. navigating properties of the trajectory need yet to be exploited. In the field of cardiac MRI, it has to be considered that Hence, the radial trajectory has to be interleaved such that the anatomy of the heart is very complex. Furthermore, the first readout of every interleave starts at the top of the sphere, which represents the shell covering all readouts. If this in many cases, the location and orientation of the heart is done sub-optimally, the image quality might be degraded by differ individually within the thorax. Up to now, only eddy current effects, and advanced density compensation is experienced operators are able to perform a comprehen- needed. In this work, an innovative 3D radial trajectory based on sive cardiac MR examination. As a consequence, the option a natural spiral phyllotaxis pattern is introduced, which features to acquire a 3D volume that covers the whole heart with optimized interleaving properties: (1) overall uniform readout high and isotropic resolution is a much desirable goal (11). distribution is preserved, which facilitates simple density com- In this configuration, some of the preparatory steps of a pensation, and (2) if the number of interleaves is a Fibonacci cardiac examination are obsolete since the complexity of number, the interleaves self-arrange such that eddy current effects are significantly reduced.