Richard Kennaway

John Innes Centre · Department of Cell and Developmental Biology

Growth coordination between cell layers is essential for development of most multicellular organisms. Coordination may be mediated by molecular signaling and/or mechanical connectivity between cells, but how genes modify mechanical interactions between layers is unknown. Here we show that genes driving brassinosteroid synthesis promote growth of in...

Plant development depends on coordination of growth between different cell layers. Coordination may be mediated by molecular signalling or mechanical connectivity between cells, but evidence for genetic control via direct mechanics has been lacking. We show that a brassinosteroid-deficient dwarf mutant of the aquatic plant Utricularia gibba has twi...

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...

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...

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...

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...

Subtle origin for complex shapes The cup-shaped leaves of carnivorous plants have evolved multiple times from ancestors with flat leaves. Studying development of the carnivorous trap in the humped bladderwort, Utricularia gibba , Whitewoods et al. identified genes similar to those expressed in surfaces of flat leaves (see the Perspective by Moulton...

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...

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...

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...

A response to "Mechanical regulation of organ asymmetry in leaves" by Jiyan Qi et al, Nature Plants, 2017, 10.1038/s41477-017-0008-6.

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...

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...

ELife digest Plant and animal organs come in many different shapes, from pitcher-shaped leaves and butterfly wings, to orchid flowers and the convoluted shape of the brain. Unlike pottery or sculpture, no external hand guides the formation of these biological structures; they arise on their own, through sheets of cells developing into particular th...

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...

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.

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...

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...

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.

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...

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...

A movie of the growth illustrated in Figure 7 (F). (MOV)

A movie of the growth illustrated in Figure 6 (D–E). (MOV)

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...

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...

Higher resolution version of Figure S1A (clones at 300 h/day 12.5). (9.03 MB TIF)

Higher resolution version of Figure S1D (clones at 420 h/day 17.5). (9.04 MB TIF)

Higher resolution version of Figure S1D (clones at 420 h/day 17.5). (9.07 MB TIF)

Higher resolution version of Figure S1A (clones at 300 h/day 12.5). (9.02 MB TIF)

Higher resolution version of Figure S1C (clones at 380 h/day 16). (9.07 MB TIF)

Higher resolution version of Figure S1B (clones at 340 h/day 14). (9.03 MB TIF)

Higher resolution version of Figure S1C (clones at 380 h/day 16). (9.15 MB TIF)

Higher resolution version of Figure S1E (clones at 460 h/day 19). (9.07 MB TIF)

(A) Data on clonal analysis. (B) Snapdragon model. (0.09 MB PDF)

OPT image of flower bud at day 14 (relates to Figure 2 ). (1.18 MB MOV)

Higher resolution version of Figure S1B (clones at 340 h/day 14). (8.99 MB TIF)

OPT image of flower bud at day 17 (relates to Figure 2 ). (1.78 MB MOV)

OPT image of flower bud at day 20 (relates to Figure 2 ). (1.28 MB MOV)

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...

OPT image of flower bud at day 10 (relates to Figure 2 ). (0.68 MB MOV)

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)

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)

Higher resolution version of Figure S1E (clones at 460 h/day 19). (9.03 MB TIF)

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...

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...

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...

OPT image of flower bud at day 12 (relates to Figure 2 ). (1.03 MB MOV)

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)

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)

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...

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...

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...

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

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...

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...

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...

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...

-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...

Without Abstract

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...

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...

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...

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...

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.

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...

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...

We describe a method for synthesizing deaf signing animations from a high-level description of signs in terms of the HamNoSys transcription system. 1

Orthogonal term rewrite systems do not currently have any semantics other than syntactically-based ones such as term models and event structures. For a functional language which combines lambda calculus with term rewriting, a semantics is most easily given by translating the rewrite rules into lambda calculus and then using well-understood semantic...

ViSiCAST is a major new project funded by the Euro-pean Union, aiming to provide improved access to ser-vices and facilities for deaf citizens through sign lan-guage presented by a virtual human, or avatar. We give here an outline of the project, and describe early work in the area of linguistics and language processing. This work covers two distin...

Currying is a transformation of term rewrite systems which may contain symbols of arbitrary arity into systems which contain only nullary symbols, together with a single binary symbol called application. We show that for all term rewrite systems (whether orthogonal or not) the following properties are preserved by this transformation: strong normal...

In orthogonal expression reduction systems, a common generalization of term rewriting and #-calculus, we extend the concepts of normalization and needed reduction by considering, instead of the set of normal forms, a set S of "results". When S satisfies some simple axioms, we prove the corresponding generalizations of some fundamental theorems: the...

It is known that predictions about individuals from statistical data about the population are in general unreliable. However, the size of the problem is not always realised. For a number of ways of predicting information about one variable from another with which it is correlated, we compute the reliability of such predictions. For the bivariate no...

We describe an experiment in robot control, using a simulated six-legged robot. The robot, herein called Archy, is capable of standing, resisting disturbing forces, and walking over uneven terrain and up and down a staircase. It can continue to stand up and control its body position and orientation even when some legs are removed. The control syste...

Several authors have investigated the correspondence between graph rewriting and term rewriting. Almost invariably they have considered only acyclic graphs. Yet cyclic graphs naturally arise from certain optimisations in implementing functional languages. They correspond to infinite terms, and their reductions correspond to transfinite term reducti...

In functional language implementation, there is a folklore belief that there is a conflict between implementing call-by-need semantics and parallel evaluation. In this note we illustrate this by proving that reduction algorithms of a certain general and commonly used form which give call-by-need semantics offer very little parallelism. The analysis...

We describe several approaches to visualising data contained in log files which record the stream of events from various simulation applications. Besides identifying several existing useful techniques, we also report experience with the use of VRML 2.0 to reanimate log files into three-dimensional movies of the events they record. Reanimation is a...