Program

Evolution by natural selection has resulted in a remarkable diversity of organismal form that has long fascinated scientists. Despite the essential role of the phenotype in providing a selective advantage in a given ecological setting, a formal, mathematical scheme to quantify organismal form and relate it to both the genotype and the underlying developmental genetics remains absent. In this presentation we will discuss the diversity in beak form in the Darwin’s Finches of the Galápagos Islands, and show that the differences in beak morphology across these species are quantitatively accounted for by the mathematical group of affine transformations. Specifically, all beak shapes of Ground Finches (genus Geospiza) are related by scaling transformations (a subgroup of the affine group), and the same relationship holds true for all the beak shapes of other finches. This analysis shows that the beak shapes within each of these groups differ only by their scales, such as length and depth, which are genetically controlled by Bmp4 and Calmodulin. As biological shape evolves through the demands of selection on functional capacities in a given environmental context, we discuss the role of mechanics in the selection of beak shapes in natural populations. In particular, we show that beak fracture avoidance is key to selection on beak form, with taller and wider beaks being able to withstand higher forces and being enhancing survival in periods of drought by allowing birds to utilize bigger and harder seeds. We will conclude by discussing possible constraints (such as biomechanics) on beak shape that may explain the observed morphological group structure.

Humans are visual animals and the prowess of the human visual system is well seen in the domain of object recognition.   People rapidly recognize an extraordinarily large number of objects from multiple views, despite partial oculusion, and under a variety of other degradations.  This talk is about how babies and toddlers build this recognition system, and more specifically about how they build abstract visual representations of the geometric structure of 3-dimensional objects.   It is a story about weird loops and cascades in behavior (and the brain) and about how human visual representations depend on more than vision -- on hands and actions, on words and culture, and even on play.

Every life form is a semiotic system, that is, a system using signs, e.g., for information processing, communication, or construction.  In the presentation I will discuss the role of shapes in biological semiosis. To keep the discussion tractable, we focus on semantic issues and start with a couple of questions: Can a shape have a meaning? How can we distinguish a meaningful shape from a shape without a meaning? Are some shapes more suitable for semiosis than other shapes? To approach such questions I will first review ideas formulated some while ago very near this symposium site that meaning is closely related to a code, which is a contingent relation or mapping, i.e., a relation that could be different under a different context. Then, I will show how these ideas can be relatively easily (at least partially) formalized leading to a theory that can be matched to data. The basic idea is to formalize semiotic concepts with respect to a physically grounded description of a (biological) system, which is a description accessible by scientific physical experiments. With such an approach the study of shapes as signs is not just using the semiotic term "sign'' metaphorically, but rather provides a transdisciplinary structured science concept of a sign that is precisely formulated and can be based on scientific experiments.

The invariable connection between structure and function has lead biologists to use protein shapes to understand their intricate mechanisms of action. Structural biology utilizes an approach in which the determination of macromolecular shape provides insight into the fundamental workings of these proteins in health and disease. Here we give recent examples from our laboratories, which study the molecular mechanisms underlying two cellular processes commonly aberrant in cancer, cell cycle regulation and DNA damage response. In an attempt to understand how protein complexes function in living cells, we will provide examples and experimental strategies on how to infer potential function from knowledge of structure.
Cellular cycles of growth and division are carefully coordinated by a set of regulatory proteins, whose functions are controlled by phosphorylation. We study how modification of target proteins by phosphorylation changes their shapes and detail how these conformational changes are converted into signals that drive cell proliferation. We will subsequently review a different phospho-binding protein, which serves to examine DNA for the presence of unwanted modifications. When assembled at the site of lesions, these repair complexes build up molecular machines that help coordinate the repair response. The structural studies provide the shape and hence provide clear functional constraints on how these machines operate.

Recent years have seen a remarkable resurgence of interest in quantitative aspects of biological variation and in the interfaces between evolution, genetics and development. As a result, the evolution of organismal shapes can be studied with a range of new approaches. My lab is using morphometric analyses of shape as a "common currency" to integrate studies of genetic and developmental and phylogenetic aspects of morphological evolution. Analyses in a range of organisms, from plants and insects to humans, have indicated that genetic variation of shape is highly structured. Some aspects can respopnd readily to selection, whereas others cannot. There appear to be many genes involved in the variation of shape, but allelic effects tend to be small. The structure of body plans can be used to extract information about development, for instance, by studying the covariation of asymmetries. Such studies indicate varied patterns of integration or modularity, depending on the particular system under study. In some cases, these patterns coincide with patterns of genetic covariation, and thus suggests a developmental origin for it, but in other cases the patterns are inconsistent, suggesting that the spatial pattern of gene action has other origins. Phylogenetic analyses of evolutionary diversification add a large-scale perspective to these considerations. Multi-level analyses suggest that evolutionary processes may be directed to a considerable degree by intrinsic organismal factors such as development. Yet, there is also clear evidence of selection. Unravelling the relative contributions of these factors will remain a challenge for future studies.

Rapid changes in cell shape, plasticity and motility take place during the development of vertebrate organisms. Ultimately the majority of cells comprising terminally differentiated tissues such as the neurons of the brain or the hepatocytes of the liver acquire a distinctive shape, the maintenance of which is required for normal tissue homeostasis and function. Pr. Goldman and his team are interested in identifying the factors responsible for the regulation of the dynamic changes in cellular form and behavior during early development, as well as those factors involved in the establishment and maintenance of the shape and mechanical integrity of terminally differentiated cells.  They are specifically investigating the structure and function of intermediate filament (IF) cytoskeletal networks in these processes. The structure of such filaments will be in particular presented by Pr. Aebi, whose team, among others, have demonstrated that IFs can be stretched up to 3.5-fold with a maximum force of ~3.5 nanoNewton before they rupture. The molecular origin of this 250% extension resides in the nature of the elementary building block of IFs, i.e. the a-helical coiled-coil dimer that can be converted into b-sheet-type structures upon stretching. This property of IFs is termed strain hardening, i.e. upon application of stress the filament suspension becomes more viscoelastic. This property renders IFs distinct from MFs and MTs, which break without a similar response when strain is increased. As a consequence, the IF cytoskeleton provides cells with compliance to small deformations and, at the same time, stiffens cells when large stresses are applied.Pr. Aebi team is now working on showing that alterations in the architecture of the IF cytoskeleton, i.e. by introducing mutant IF proteins into living cells, have a direct impact on their mechano-biological properties (i.e. cell shape and plasticity).

Fractals are shapes that are similar to themselves at many different scales. Unlike the squares and triangles of Euclid, we can use fractals to model recursive forms in nature.  Some cultural artifacts also have recursive forms; in particular African design is rife with self-similar shapes. It is thus tempting to posit that African cultures are somehow “more natural” than those which utilize Euclidean geometry. However such assertions have no empirical basis: in fact most indigenous societies emphasize Euclidean shapes, and many urban decorations emphasize imitation of nature. Thus we need a different theory; one we approach by examining the concept of agency in both natural and cultural morphogenesis. Using the history of one particular class of structures, those generated by recursive application of the golden ratio, we will illustrate the process that moves designs towards either recursive or non-recursive forms.

Conventional accounts of  golden ratio structures claim this form was first discovered by ancient Greek mathematicians, who applied it to classical arts and architecture.  But there is no evidence that ancient Greeks applied the ratio to visual form, nor that it was used in later classical designs. We posit an alternative origin of the golden ratio structures in African designs, starting in the architecture of sub-Saharan African, and eventually finding its way to Europe via Egypt. The revisionist account of the ancient Greeks as founders of recursive form is thus an example of ethically suspect cultural agency. While nature exhibits agency without intentionality, and individuals exhibit agency with intentions, cultural agency inhabits a grey zone in which ethically culpable acts can occur without accountability. We conclude by calling for a more reflexive approach on the part of both scientists and designers; one which moves the agency of both nature and culture towards the generation of socially just forms of living.

Brainstorming will take place in the groups of 10-15 participants and animated by a couple invited speakers. Anyone can propose a topic to be discussed, either via blog before the symposium, or during the initial warm-up period of the brainstorming session. The results and ideas of each group will be presented to everyone at the end of the brainstorming session.