Computing an organism: on the interface between informatic and dynamic processes.

The importance of interactions between processes at diverse space and time scales in biological information processing is a recurrent theme in the work of Michael Conrad (BioSystems, 1995: 35, 157-160; BioSystems, 1999: 52, 99-100). In this paper I present some results of explicit computational models that aim to capture and exploit some of the essential features of such multi-level processes. In the model formulation, I try to minimize the explicit definition of inter-level interactions, while providing the possibility of such interactions to develop. As often argued by Conrad inter-level interactions limit programmability. Indeed, we use an evolutionary process to derive the specific models. We study morphogenesis. We show that the interplay between cell adhesion and cell differentiation provides interesting mechanisms for morphogenesis. We also show that the interplay can both reduce and enhance small random fluctuations. We show that unequal cell cleavage in the early embryo-genesis reduces inter-individual variation of the morphemes developed from the same 'genome'. Our results suggest that, during evolution, the interplay between levels is exploited while it is at the same time reduced so as to give a certain primacy to inherited information.

[1]  L. Segel,et al.  Computing an organism , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Alvy Ray Smith,et al.  Plants, fractals, and formal languages , 1984, SIGGRAPH.

[3]  Paulien Hogeweg,et al.  Phototaxis during the slug stage of Dictyostelium discoideum: a model study , 1999, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[4]  M. Huynen,et al.  Smoothness within ruggedness: the role of neutrality in adaptation. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[5]  A. Lindenmayer,et al.  Developmental algorithms for multicellular organisms: a survey of L-systems. , 1975, Journal of theoretical biology.

[6]  P. Hogeweg,et al.  Modelling Morphogenesis: From Single Cells to Crawling Slugs. , 1997, Journal of theoretical biology.

[7]  Erkki Ruoslahti,et al.  Stretching Is Good for a Cell , 1997, Science.

[8]  A. Lindenmayer Mathematical models for cellular interactions in development. II. Simple and branching filaments with two-sided inputs. , 1968, Journal of theoretical biology.

[9]  M. Conrad,et al.  Cross-scale information processing in evolution, development and intelligence. , 1996, Bio Systems.

[10]  L Wolpert,et al.  Mechanisms for positional signalling by morphogen transport: a theoretical study. , 1998, Journal of theoretical biology.

[11]  A. Lindenmayer Mathematical models for cellular interactions in development. I. Filaments with one-sided inputs. , 1968, Journal of theoretical biology.

[12]  H. Meinhardt,et al.  Pattern formation by local self-activation and lateral inhibition. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[13]  M Conrad Cross-scale interactions in biomolecular information processing. , 1995, Bio Systems.

[14]  Aristid Lindenmayer,et al.  Mathematical Models for Cellular Interactions in Development , 1968 .

[15]  P. Hogeweg,et al.  How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[16]  P. Hogeweg Shapes in the Shadow: Evolutionary Dynamics of Morphogenesis , 1999, Artificial Life.

[17]  Paulien Hogeweg,et al.  Multilevel processes in evolution and development: Computational models and biological insights , 2002 .

[18]  R V Solé,et al.  Phenotypic and dynamical transitions in model genetic networks II. Application to the evolution of segmentation mechanisms , 2001, Evolution & development.

[19]  M. Huynen,et al.  Pattern generation in molecular evolution: Exploitation of the variation in RNA landscapes , 1994, Journal of Molecular Evolution.

[20]  M. Huynen,et al.  Neutral evolution of mutational robustness. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Paulien Hogeweg,et al.  On searching generic properties of non generic phenomena: an approach to bioinformatic theory formation , 1998 .

[22]  P. Hogeweg,et al.  Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation. , 2000, Journal of theoretical biology.

[23]  J. McNally,et al.  Three-dimensional in vivo analysis of Dictyostelium mounds reveals directional sorting of prestalk cells and defines a role for the myosin II regulatory light chain in prestalk cell sorting and tip protrusion. , 2000, Development.

[24]  P. Hogeweg,et al.  Migration and thermotaxis of dictyostelium discoideum slugs, a model study , 1999, Journal of theoretical biology.

[25]  Glazier,et al.  Simulation of the differential adhesion driven rearrangement of biological cells. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[26]  A. Turing The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[27]  Przemyslaw Prusinkiewicz,et al.  The Algorithmic Beauty of Plants , 1990, The Virtual Laboratory.

[28]  C. S. Chen,et al.  Geometric control of cell life and death. , 1997, Science.

[29]  A C Maggs,et al.  Diffusion and formation of microtubule asters: physical processes versus biochemical regulation. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Paulien Hogeweg,et al.  A model study on biomorphological description , 1974, Pattern Recognit..

[31]  H. Nishida,et al.  Maternal cytoplasmic factors for generation of unique cleavage patterns in animal embryos. , 1999, Current topics in developmental biology.