Richard Kennaway

Richard Kennaway
John Innes Centre · Department of Cell and Developmental Biology

D.Phil.

About

139
Publications
19,704
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2,848
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Introduction
I am primarily engaged in designing, developing, and supporting the finite element software that my biological colleagues use to model the growth of plant tissues. I am also involved with the development of software for animation of sign languages, and am currently working on a project in procedural architecture (architecture in its primary sense, the construction of buildings). I have also worked on rewriting systems, lambda calculus, and other things which this box is too small to contain.
Additional affiliations
October 2013 - present
John Innes Centre
Position
  • Senior Researcher
July 1981 - August 2013
University of East Anglia
Position
  • Senior Researcher
December 1979 - January 1981
Education
September 1976 - December 1979
University of Oxford
Field of study
  • Mathematics
September 1973 - June 1976
The University of Edinburgh
Field of study
  • Mathematics

Publications

Publications (139)
Article
A behavioral illusion is a regularity of behavior that appears to reflect something about the functional characteristics of an organism when it does not. This illusion occurs when the methods appropriate to the study of an open-loop or zero feedback (Z)-system are used to study the behavior of what is, in fact, a closed-loop or negative feedback (N...
Article
Shared systems in leaf development The long, narrow leaves of grasses look rather different from the often shorter, flatter leaves of eudicot plants. Richardson et al . combined developmental genetics and computational modeling to reveal that these two types of leaves, which are widely separated by evolution, have more in common than expected. Expr...
Preprint
Full-text available
In utility theory, certain infinite gambles pose problems, of which the St. Petersberg paradox is the most well-known. Various methods have been used to eliminate the paradoxes, including the supposition that utility is bounded, or that probabilities must decline faster than utility so as to always result in finite expectation values, or simply exc...
Chapter
Full-text available
Current methods of detecting causal relationships from data rely on analysing the patterns of correlation among the variables. Given some basic assumptions about how causal relationships constrain these patterns, this allows causal inferences to be made. I demonstrate that one commonly used assumption, called Faithfulness (roughly, where there is c...
Article
Leaves vary from planar sheets and needle-like structures, to elaborate cup-shaped traps. Here we show that in the carnivorous plant Utricularia gibba, the upper leaf (adaxial) domain is restricted to a small region of the primordium which gives rise to the trap’s inner layer. This restriction is necessary for trap formation, as ectopic adaxial act...
Article
Full-text available
Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3...
Article
Full-text available
Differential growth is the driver of tissue morphogenesis in plants, and also plays a fundamental role in animal development. Although the contributions of growth to shape change have been captured through modelling tissue sheets or isotropic volumes, a framework for modelling both isotropic and anisotropic volumetric growth in three dimensions ove...
Article
Full-text available
A developing plant organ exhibits complex spatiotemporal patterns of growth, cell division, cell size, cell shape, and organ shape. Explaining these patterns presents a challenge because of their dynamics and cross-correlations, which can make it difficult to disentangle causes from effects. To address these problems, we used live imaging to determ...
Article
A response to "Mechanical regulation of organ asymmetry in leaves" by Jiyan Qi et al, Nature Plants, 2017, 10.1038/s41477-017-0008-6.
Article
Full-text available
The mechanisms by which organisms acquire their sizes and shapes through growth was a major focus of D'Arcy Thompson's book On Growth and Form. By applying mathematical and physical principles to a range of biological forms, Thompson achieved fresh insights, such as the notion that diverse biological shapes could be related through simple deformati...
Article
Full-text available
Boundary domain genes, expressed within or around organ primordia, play a key role in the formation, shaping, and subdivision of planar plant organs, such as leaves. However, the role of boundary genes in formation of more elaborate 3D structures, which also derive from organ primordia, remains unclear. Here we analyze the role of the boundary doma...
Article
Full-text available
Out-of-plane tissue deformations are key morphogenetic events during plant and animal development that generate 3D shapes, such as flowers or limbs. However, the mechanisms by which spatiotemporal patterns of gene expression modify cellular behaviours to generate such deformations remain to be established. We use the Snapdragon flower as a model sy...
Article
Full-text available
Fruits exhibit a vast array of different 3D shapes, from simple spheres and cylinders to more complex curved forms; however, the mechanism by which growth is oriented and coordinated to generate this diversity of forms is unclear. Here, we compare the growth patterns and orientations for two very different fruit shapes in the Brassicaceae: the hear...
Article
Full-text available
In a previous paper we have established the theory of trans-finite reduction for orthogonal term rewriting systems. In this paper we perform the same task for the lambda calculus. This results in several new BShm-like models of the laznbda calculus, and new descriptions of existing models.
Article
We present a novel approach to combined textual and visual programming by allowing visual, interactive objects to be embedded within textual source code and segments of source code to be further embedded within those objects. We retain the strengths of text-based source code, while enabling visual programming where it is beneficial. Additionally, e...
Technical Report
Full-text available
We demonstrate that the Faithfulness property that is assumed in much causal analysis is robustly violated for a large class of systems of a type that occurs throughout the life and social sciences: control systems. These systems exhibit correlations indistinguishable from zero between variables that are strongly causally connected, and can show ve...
Chapter
The article surveys the philosophically-based artificial languages of the 17th century, the emergence of international auxiliary languages from the late 19th century onward, most notably Esperanto, the construction of languages for the purposes of fiction or recreation from the later 20th century to the present, and programming languages.
Article
Full-text available
A major challenge in biology is to understand how buds comprising a few cells can give rise to complex plant and animal appendages like leaves or limbs. We address this problem through a combination of time-lapse imaging, clonal analysis, and computational modeling. We arrive at a model that shows how leaf shape can arise through feedback between e...
Conference Paper
Full-text available
We present a small-scale study that provides detailed timing information for individual sign parameters in natural signing with a time resolution of 1/50 of a second as well as the method and tools used to collect these data. The avatar system was improved to be able to play back signing annotated in a combination of symbolic movement description a...
Data
A movie of the growth illustrated in Figure 7 (F). (MOV)
Data
A movie of the growth illustrated in Figure 6 (D–E). (MOV)
Article
Full-text available
A major problem in biology is to understand how complex tissue shapes may arise through growth. In many cases this process involves preferential growth along particular orientations raising the question of how these orientations are specified. One view is that orientations are specified through stresses in the tissue (axiality-based system). Anothe...
Data
Clonal patterns and growth data for wild-type shaped petals, relates to Figure 3. (A–E) Clones on petals of several flowers induced at a range of stages: (A) 300 h (day 12.5), (B) 340 h (day 14), (C) 380 h (day 16), (D) 420 h (day 17.5), and (E) 460 h (day 19), warped to a mean petal shape and overlaid, with a different colour used for clones from...
Data
Higher resolution version of Figure S1A (clones at 300 h/day 12.5). (9.03 MB TIF)
Data
Higher resolution version of Figure S1D (clones at 420 h/day 17.5). (9.04 MB TIF)
Data
Higher resolution version of Figure S1D (clones at 420 h/day 17.5). (9.07 MB TIF)
Data
Higher resolution version of Figure S1A (clones at 300 h/day 12.5). (9.02 MB TIF)
Data
Higher resolution version of Figure S1C (clones at 380 h/day 16). (9.07 MB TIF)
Data
Higher resolution version of Figure S1B (clones at 340 h/day 14). (9.03 MB TIF)
Data
Higher resolution version of Figure S1C (clones at 380 h/day 16). (9.15 MB TIF)
Data
Higher resolution version of Figure S1E (clones at 460 h/day 19). (9.07 MB TIF)
Data
Full-text available
(A) Data on clonal analysis. (B) Snapdragon model. (0.09 MB PDF)
Data
OPT image of flower bud at day 14 (relates to Figure 2 ). (1.18 MB MOV)
Data
Higher resolution version of Figure S1B (clones at 340 h/day 14). (8.99 MB TIF)
Data
OPT image of flower bud at day 17 (relates to Figure 2 ). (1.78 MB MOV)
Data
OPT image of flower bud at day 20 (relates to Figure 2 ). (1.28 MB MOV)
Data
Growth data for each region (relates to Figure 3). An Excel table showing the growth along the principal direction of growth (Kmax), the growth perpendicular to that within the plane of the petal surface (Kmin), the anisotropy (Kmax/Kmin), and the orientation (θ) of the principal direction of growth for each region (see Figure S12) for each step (3...
Data
OPT image of flower bud at day 10 (relates to Figure 2 ). (0.68 MB MOV)
Data
Growth model of the cyc dich div triple mutant (scale constant throughout). LIP in light grey, PLT in dark grey, −organisers in cyan, +organiser in green. Coloured circles (virtual clones) induced at about 14 d (relates to Figure 4). (1.31 MB MOV)
Data
Final growth model of wild-type corolla (scale constant throughout). Factors shown as in Video S8. Coloured circles (virtual clones) induced at about 14 d (relates to Figure 9 and to Model 7 in Text S1B). (1.33 MB MOV)
Data
Higher resolution version of Figure S1E (clones at 460 h/day 19). (9.03 MB TIF)
Data
Grids used for clonal analysis of wild-type petals, relates to Figure 3 and Tables S1,S2. (A–D) Grids used for the period 300–340 h: (A) Dorsal lobe, (B) Lateral lobe, (C) Ventral lobe, and (D) Half tube. (E–H) Grids used for the period 340–380 h: (E) Dorsal lobe, (F) Lateral lobe, (G) Ventral lobe, and (H) Half tube. (I–L) Grids used for the perio...
Data
Clonal patterns for dorsoventral mutant petals, relates to Figures 4 and 5. (A–E) Clones on lobes from several cyc dich double mutant flowers induced at a range of stages: (A) 300 h (day 12.5), (B) 330 h (day 14), (C) 350 h (day 15), (D) 380 h (day 16), and (E) 400 h (day 17) (note that developmental timing does not correlate perfectly with wild ty...
Data
Average sector ellipses by region (relates to Figure 3). An Excel table showing the lengths of the major axis (Emaj) and minor axis (Emin) and the orientation (θ) for the average sector ellipse for each region (see Figure S12; θ is given in radians relative to the x-axis) for each stage (300 h, 340 h, 380 h, 420 h, and 460 h). There are two sets of...
Data
OPT image of flower bud at day 12 (relates to Figure 2 ). (1.03 MB MOV)
Data
Growth model of the cyc dich double mutant (scale constant throughout). LIP in light grey, PLT in dark grey, DIV in yellow, −organisers in cyan, +organiser in green. Coloured circles (virtual clones) induced at about 14 d (relates to Figure 5). (1.05 MB MOV)
Data
First growth model of wild-type corolla (scale constant throughout). LIP in light grey, PLT in dark grey, DIV in yellow, CYC in red, DICH in brown, −organisers in cyan, +organiser in green. Coloured circles (virtual clones) induced at about 14 d (relates to Figure 6 and to Model 3 in Text S1B). (1.11 MB MOV)
Article
Full-text available
The mechanisms by which genes control organ shape are poorly understood. In principle, genes may control shape by modifying local rates and/or orientations of deformation. Distinguishing between these possibilities has been difficult because of interactions between patterns, orientations, and mechanical constraints during growth. Here we show how a...
Article
Full-text available
We outline the main features of our synthetic virtual human sign language system, JASigning. We describe how we have extended its input notation, SiGML, to allow explicit control of performance time, and we describe our initial steps on the path to integrating virtual human sign language performance into annotation tools, where it may be compared w...
Article
Full-text available
Correlated variation in shape and size (allometry) is a major component of natural diversity. We examined the evolutionary and genetic basis for allometry using leaves and flower petals of snapdragon species (Antirrhinum). A computational method was developed to capture shape and size variation in both types of organ within the Antirrhinum species...
Article
Full-text available
The present work applies a control architecture proposed by W.T. Powers [3, 4], to several problems in robotics, and suggests that it may have wide practical applicability. The architecture is called (Hierarchical) Perceptual
Article
Full-text available
Sign languages are the native languages for many pre-lingually deaf people and must be treated as genuine natural languages worthy of academic study in their own right. For such pre-lingually deaf, whose familiarity with their local spoken language is that of a second language learner, written text is much less useful than is commonly thought. This...
Article
Full-text available
Written information is often of limited accessibility to deaf people who use sign language. The eSign project was undertaken as a response to the need for technologies enabling efficient production and distribution over the Internet of sign language content. By using an avatar-independent scripting notation for signing gestures and a client-side we...
Article
Full-text available
When animation of a humanoid figure is to be generated at run-time, instead of by replaying pre-composed motion clips, some method is required of specifying the avatar's movements in a form from which the required motion data can be automatically generated. This form must be of a more abstract nature than raw motion data: ideally, it should be inde...
Chapter
Dactl is an experimental language programming language based on fine grain graph transformations. It was developed in the context of a large parallel reduction machine project. The design of the language is outlined, and examples given of its use both as a compiler target language and as a programming language. Dactl has a formal semantics and stab...
Chapter
-definability of term rewriting systems has been an open question. Berarducci and Bhm show that canonical systems are translated into the -calculus. However, they do not present a theory which can formalize their translation. In this paper, we adapt Bhm's separability theory for -definability. A term rewriting system version of separability, called...
Conference Paper
Graph rewriting (also called reduction) as defined in Wadsworth [1971] was introduced in order to be able to give a more efficient implementation of functional programming languages in the form of lambda calculus or term rewrite systems: identical subterms are shared using pointers. Several other authors, e.g. Ehrig [1979], Staples [1980a,b,c], Rao...
Conference Paper
Lean is an experimental language for specifying computations in terms of graph rewriting. It is based on an alternative to Term Rewriting Systems (TRS) in which the terms are replaced by graphs. Such a Graph Rewriting System (GRS) consists of a set of graph rewrite rules which specify how a graph may be rewritten. Besides supporting functional prog...
Conference Paper
Full-text available
Rewriting is the repeated transformation of a structured object according to a set of rules. This simple concept has turned out to have a rich variety of elaborations, giving rise to many di erent theoretical frameworks for reasoning about computation. Aside from its theoretical importance, rewriting has also been a significant influence on the des...
Article
Full-text available
We present an overview of research at UEA into the animation of sign language using a gesture notation, outlining applications that have been developed and key aspects of the implementation. We argue that the requirements for virtual human signing involve the development of expressive characters. Although the prin- cipal focus of work has been on s...
Conference Paper
Full-text available
We discuss our experience with automatic synthesis of animations of deaf signing from an avatar-independent notation for signing gestures, and consider principles that a notation designed for synthetic animation should satisfy.
Conference Paper
We investigate the degree of parallelism (or modularity) in the hyperbalanced λ-calculus, λH, a subcalculus of λ-calculus containing all simply typable terms (up to a restricted η-expansion). In technical terms, we study the family relation on redexes in λH, and the contribution relation on redex-families, and show that the latter is a forest (as a...
Conference Paper
We investigate the degree of parallelism (or modularity) in the hyperbalanced ¿-calculus, ¿H, a subcalculus of ¿-calculus containing all simply typable terms (up to a restricted ¿-expansion). In technical terms, we study the family relation on redexes in ¿H, and the contribution relation on redex-families, and show that the latter is a forest (as a...